Computational Study Research Articles

Current developments in elastic and acoustic metamaterials science.

The concept of metamaterial recently emerged as a new frontier of scientific research, encompassing physics, materials science and engineering. In a broad sense, a metamaterial indicates an engineered material with exotic properties not found in nature, obtained by appropriate architecture either at macro-scale or at micro-/nano-scales. The architecture of metamaterials can be tailored to open unforeseen opportunities for mechanical and acoustic applications, as demonstrated by an impressive and increasing number of studies. Building on this knowledge, this theme issue aims to gather cutting-edge theoretical, computational and experimental studies on elastic and acoustic metamaterials, with the purpose of offering a wide perspective on recent achievements and future challenges. This article is part of the theme issue 'Current developments in elastic and acoustic metamaterials science (Part 1)'.

Molecular dynamics simulations of the effect of static electric field on progressive ice formation.

Ice accumulation under static electric fields presents a significant hazard to transmission lines and power grids. Contemporary computational studies of electrofreezing predominantly probed excessive electric fields (109 V/m) that are significantly higher than those typically encountered in proximity to transmission lines. To elucidate the influence of realistic electric fields (105 V/m) on ice crystallization, we run extensive molecular dynamics (MD) simulations across dual ice-water coexistence systems. Three aspects of work were accordingly examined. First, we investigated the influence of the effect of static electric fields, with a strength of 105 V/m, along three orthogonal axes on the phase transition during the encountered freezing and melting processes. Second, we established the mechanism of how the direction of an electric field, the initial ice crystallography, and the adjacent crystal planes influence the solidification process. Third, the results of our MD simulations were further post-processed to determine the dipole moment, radial distribution, and angle distribution resulting from the static electric field. Our results indicate that while weak electric fields do not cause complete polarization of liquid water molecules, they can induce a transition to a more structured ice-like geometry of the water molecules at the ice-water interphase region, particularly when applied perpendicular to the ice-water interphase. Notably, the interface adjacent to cubic ice exhibits a greater response to the electric fields than that adjacent to hexagonal ice. This is attributable to the intrinsic differences in their original hydrogen bonding networks.

Chitosan grafted with gallic acid and cerium dioxide hybrid nanocomposites as environmentally friendly corrosion inhibitors for mild steel: An experimental and computational study

Chitosan grafted with gallic acid (CS-GA), along with CS-GA doped with CeO2 nanoparticles (CS-GA-CeO2) were synthesized as novel environmentally friendly mild steel corrosion inhibitors. The formation of these derivatives was confirmed by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), hydrogen nuclear magnetic resonance spectroscopy (1H NMR), and thermal analysis (TGA). Based on potentiodynamic polarization curves (PDP) measurements, the inhibitors acted primarily as hybrid inhibitors, while following the Langmuir adsorption theory model. Scanning electron microscopy (SEM), X-ray photoelectron spectroscopy(XPS) and 3D surface profiles, confirmed that CS-GA-CeO2 adsorbed on the mild steel forming a protective layer thus preventing the invasion of corrosive media. The corrosion protection mechanism of chitosan derivatives was investigated by molecular dynamics simulations. Electrochemical measurements were used to investigate the corrosion inhibition by CS-GA and CS-GA-CeO2 on mild steel in a 3.5 % NaCl solution. At room temperature, the highest inhibition efficiency (93.58 %) was achieved at 200 ppm CS-GA-CeO2. Modified chitosan nanocomposites were confirmed as promising corrosion inhibitors.

Dinaphthodiospyrol H: a natural α-glucosidase inhibibitor extracted from Diospyros kaki L.f.

The roots of Diospyro kaki L.f., known for their anti-inflammatory, antimicrobial and antidiabetic properties, are the source of dimeric naphthoquinones, including dinaphthodiospyrol H. α-Glucosidase is an enzyme involved in regulation of blood glucose levels and its inhibition helps in the control of the postprandial hyperglycaemia. In this study, an in vitro evaluation of dinaphthodiospyrol H was carried out and the compound inhibited α-glucosidase with an IC50 value of 57.38 ± 0.87 µg/mL, revealing a significant potential that supports the traditional application of D. kaki in the treatment of diabetes mellitus. Additionally, computational studies, including docking and molecular dynamics, were used to investigate ligand-target complex and showed that the compound targets the same site with which acarbose interacts. Overall, the findings provide new basis to translate the traditional use of D. kaki into modern medicinal chemistry.

K+-Mediated vs Pd-Catalyzed Cyclotrimerization of 9,10-Didehydrotribenzo[8]annulene (TribenzoCOTyne): Stereodivergent Access to (α,α,α)- and (α,α,β)-Fragments of Cubic Graphite.

A remarkable stereodivergent cyclotrimerization of 9,10-didehydrotribenzo[8]annulene (tribenzoCOTyne) to the corresponding (α,α,α)- and (α,α,β)-benzofused derivatives has been developed by controlling the reaction conditions. While the K+-mediated cyclotrimerization afforded the (α,α,α) stereoisomer, using Pd as a catalyst resulted in the (α,α,β)-derivative. Both stereoisomers were evidenced by spectroscopic data and crystal X-Ray analysis. The (α,α,α) stereoisomer is a fragment of cubic graphite (CG), an elusive 3D carbon allotrope that contains carbon cages, since all of its sixty carbons are part of the structure of CG, and 36 constitute a part of the C48 molecular cage of CG. Experimental and computational mechanistic studies revealed that the potassium ion would play a key role as a template to favor the formation of the (α,α,α) stereoisomer.

In vitro anticancer activity of a head-to-toe constructed heterobimetallic [CoFeL]2+ metallocylinder

ABSTRACT [M2L3]-type metallo-supramolecular architectures (MSAs) are widely explored for their biological activity, whereas data on non-symmetric, heterobimetallic [MM’L3] structures is comparatively rare. [M2L3] compounds are known to form helicates and/or mesocates. Here, we report the self-assembly of a discrete non-symmetrical, heterobimetallic MSA by combination of an amine-functionalised cobalt(III)-tris((picolinamido)ethyl)amine (PICTREN) base unit with FeCl2 and 2,2’-bipyridine-5-carboxaldehyde. NMR spectroscopy in tandem with computational studies revealed the formation of a mesocate rather than a helicate. The ability of the heteromesocate to bind to DNA was examined by gel electrophoresis with pUC19 plasmid DNA, which showed DNA binding although longer incubation periods were required than found for a known DNA-interacting helicate. The mesocate displayed promising antiproliferative activity in cancer cells, including a cisplatin-resistant cell line, with IC50 values in the 17–26 μM range. Lower biological activity of the mesocate compared to a metallocylinder reference and cisplatin may be explained by differences in the DNA interactions. This work further supports efforts to establish methods with which to construct heterobimetallic complexes, establishing the utility of the self-assembly method in [M2L3]-type assemblies using the cobalt(III)-PICTREN platform as a robust building block towards more complex assemblies of the [MM’L]-type.

Advancing H-Bonding Organocatalysis for Ring-Opening Polymerization: Intramolecular Activation of Initiator/Chain End.

Organocatalytic ring-opening polymerization (ROP) of lactones is a green method for accessing renewable and biodegradable polyesters. Developing new organocatalysts with high activity and controllability is a major and challenging research topic in this field. Here, we report a series of organocatalysts to achieve a fast and controlled ROP of lactones. These catalysts incorporate (thio)urea and alkoxide in one molecule and act as initiators in the ROP. Such catalysts enable an effective intramolecular activation of initiator/chain end, as revealed by computational studies, resulting in higher activity and fewer (thio)urea loads than existing (thio)urea/alkoxide binary systems. These organocatalysts exhibit ultrahigh activity comparable to metal complexes, i.e., turnover number up to 900 and turnover of frequency up to 4860 min-1, affording polyesters with tailor-made structure, predicted molecular weights, narrow dispersity, less epimerization, and minimal transesterification. The catalyst synthesis is simple and scalable, allowing widely tuned activities of the ROP.

Ten quick tips for electrocardiogram (ECG) signal processing

The electrocardiogram (ECG) is a powerful tool to measure the electrical activity of the heart, and the analysis of its data can be useful to assess the patient’s health. In particular, the computational analysis of electrocardiogram data, also called ECG signal processing, can reveal specific patterns or heart cycle trends which otherwise would be unnoticeable by medical experts. When performing ECG signal processing, however, it is easy to make mistakes and generate inflated, overoptimistic, or misleading results, which can lead to wrong diagnoses or prognoses and, in turn, could even contribute to bad medical decisions, damaging the health of the patient. Therefore, to avoid common mistakes and bad practices, we present here ten easy guidelines to follow when analyzing electrocardiogram data computationally. Our ten recommendations, written in a simple way, can be useful to anyone performing a computational study based on ECG data and eventually lead to better, more robust medical results.

A Well-Defined Magnesium Complex of C70 6.

Controlling and understanding charge state and metal coordination in carbon nanomaterials is crucial to harnessing their unique properties. Here we describe the synthesis of the well-defined fulleride complex [{(Mesnacnac)Mg}6C70], 2, (Mesnacnac)=HC(MeCNMes)2, Mes=2,4,6-Me3C6H2, from the reaction of the β-diketiminate magnesium(I) complex [{(Mesnacnac)Mg}2] with C70 in aromatic solvents. The molecular structure of complex 2 was determined, providing the first high-quality structural study of a complex with the C70 6- ion. In combination with solution state NMR spectroscopic and DFT computational studies, the changes in geometry and charge distribution in the various atom and bond types of the fulleride unit were investigated. Additionally, the influence of the (Mesnacnac)Mg+ cations on the global and local fulleride coordination environment was examined.

Quantum chemical investigation of electronic transitions of mitorubrin azaphilones.

Fungal azaphilones are a broad class of naturally-occurring pigments with diverse applications. Among the azaphilone pigments, mitorubrins are well recognized for their antiviral, antibacterial, antifungal, antiprotozoal, antidiabetic, and antiaging activities in addition to their well-known yellow-orange color. This makes these pigments interesting candidates for use in foods, as cosmetics, and as medicines. In particular, if it is desired to modify the properties of mitorubrin-based pigments, for example by derivatization, it is essential to have an understanding of the electronic spectra of the parent molecules. We have therefore undertaken a computational study of a series of mitorubrins, comparing our computed results with experimental UV/visible spectra. Both density-functional theory (DFT) and coupled-cluster (CC2) methods have been used, and in general, the results are in very good agreement with observation. In order to provide a simple and useful picture of the spectra we analyze the stronger transitions in terms of natural transition orbitals (NTOs).

Near‐IR Emissive B–N Lewis Pair‐Functionalized Anthracenes via Selective LUMO Extension in Conjugated Dimer and Polymer

AbstractAcenes are attractive as building blocks for low gap organic materials with applications, for example, in organic light emitting diodes, solar cells, bioimaging and diagnostics. Previously, we have shown that modification of dipyridylanthracene via B–N Lewis pair fusion (BDPA) strongly redshifts the emission, while facilitating self‐sensitized reactivity toward O2 to reversibly generate the corresponding endoperoxides. Herein, we report on the further expansion of the π‐system of BDPA to a vinyl‐substituted monomer, vinylene‐bridged dimer, and a polymer with an average of 20 chromophores. The extension of π‐conjugation results in largely reduced band gaps of 1.8 eV for the dimer and 1.7 eV for the polymer, the latter giving rise to NIR emission with a maximum at 731 nm and an appreciable quantum yield of 7 %. Electrochemical and computational studies reveal efficient delocalization of the lowest unoccupied molecular orbital (LUMO) along the pyridyl‐anthracene‐pyridyl axis, which results in effective electronic communication between BDPA units, selectively lowers the LUMO, and ultimately narrows the band gap. Time‐resolved emission and transient absorption (TA) measurements offer insights into the pertinent photophysical processes. Extension of π‐conjugation also slows down the self‐sensitized formation of endoperoxides, while significantly accelerating the thermal release of singlet oxygen to regenerate the parent acenes.

New theoretical insights on the nonradiative relaxation mechanism of the core structure of mycosporines: The amino-cyclohexenone central template.

We present a comprehensive computational study describing the excited state dynamics and consequent photostability of amino-cyclohexenone (ACyO), the central template of mycosporine systems, widely recognized for their photoprotection of aquatic species. Photoexcitation to the first excited electronic state (S1, 1nπ*) of ACyO is considered an optically dark transition, while photoexcitation to the second excited electronic state (S21ππ*) is an optically bright 1ππ* transition and largely responsible for UV absorption properties of this molecule. We show that following initial photoexcitation to S2, ACyO relaxes via two competing deactivation mechanisms, each mediated by an S1/S0 conical intersection, which directs the excited state population to the electronic ground state (S0). Our abinitio computational results are supported with nonadiabatic dynamics simulation results, yielding an excited state lifetime of ∼280fs for this system in vacuo. These results explain the inherent photostability of this core structure, commonplace in a wide range of microorganisms.

High Milling Time Influence on the Phase Stability and Electrical Properties of Fe50Mn35Sn15 Heusler Alloy Obtained by Mechanical Alloying

Fe50Mn35Sn15 Heusler alloy, obtained by mechanical alloying, was subjected to larger milling times in the range of 30–50 h to study the phase stability and morphology. X-ray diffraction studies have shown that the milled samples crystallise in a disordered A2 structure. The A2 structure was found to be stable in the milling range studied, contrary to the computation studies performed on this composition. Using Rietveld refinements, the lattice parameter, mean crystallite size, and lattice strain were computed. The nature of the obtained phases by milling was found to be nanocrystalline with values below 50 nm. A linear increase rate of 0.00713 (h−1) was computed for lattice strain as the milling time increased. As the milling time increases, the lattice parameter of the cubic Heusler was found to have a decreasing behaviour, reaching 2.9517 Å at 50 h of milling. The morphological and elemental distribution—characterised by scanning electron microscopy and energy-dispersive X-ray spectroscopy—evidenced Mn and Sn phase clustering. As the milling time increased, the morphology of the sample was found to change. The Mn and Sn cluster size was quantified by elemental line profile. Electrical resistivity evolution with milling time was analysed, showing a peak for 40 h of milling time.

Accelerating Relativistic Exact-Two-Component Density Functional Theory Calculations with Graphical Processing Units.

Numerical integration of the exchange-correlation potential is an inherently parallel problem that can be significantly accelerated by graphical processing units (GPUs). In this Letter, we present the first implementation of GPU-accelerated exchange-correlation potential in the GauXC library for relativistic, 2-component density functional theory. By benchmarking against copper, silver, and gold coinage metal clusters, we demonstrate the speed and efficiency of our implementation, achieving significant speedup compared to CPU-based calculations. One GPU card provides computational power equivalent to roughly 400 CPU cores in the context of this work. The speedup further increases for larger systems, highlighting the potential of our approach for future, more computationally demanding simulations. Our implementation supports arbitrary angular momentum basis functions, enabling the simulation of systems with heavy elements and providing substantial speedup to relativistic electronic structure calculations. This advancement paves the way for more efficient and extensive computational studies in the field of density functional theory.

Chiral Brønsted Acid-Catalyzed Intramolecular Asymmetric Dearomatization Reaction of Indoles with Cyclobutanones via Cascade Friedel-Crafts/Semipinacol Rearrangement.

The highly efficient synthesis of chiral indolines fused with an azabicyclo[2.2.1]heptanone moiety is achieved by an asymmetric dearomatization reaction of indoles with cyclobutanones. A new chiral imidodiphosphorimidate (IDPi) catalyst is synthesized and exhibits extraordinary activity in promoting a cascade Friedel-Crafts/semipinacol rearrangement. Target molecules are prepared in good yields (up to 95%) with excellent enantioselectivity (up to 98% ee) with operational convenience. Combined experimental and computational studies provide detailed mechanistic insights into the energy landscape and origin of the stereochemical induction of the reaction.

Integrating Blood Biomarkers and Marine Brown Algae-Derived Inhibitors in Parkinson's Disease: A Multi-scale Approach from Interactomics to Quantum Mechanics.

Parkinson's disease (PD) involves alpha-synuclein accumulation according to Braak's pattern, with diverse clinical progressions that complicate diagnosis and treatment. We aimed to correlate Braak's pattern with rapid progressive PD to identify blood-based biomarkers and therapeutic targets exploiting brown algae-derived bioactives for potential treatment. We implemented a systematic workflow of transcriptomic profiling, co-expression networks, cluster profiling, transcriptional regulator identification, molecular docking, quantum calculations, and dynamic simulations. The transcriptomic analyses exhibited highly expressed genes at each Braak's stage and in rapidly progressive PD. Co-expression networks for Braak's stages were built, and the top five clusters from each stage displayed significant overlap with differentially expressed genes in rapidly progressive PD, indicating shared biomarkers between the blood and the PD brain. Further investigation showed, NF-kappa-B p105 as the master transcriptional regulator of these biomarkers. Molecular docking screened phlorethopentafuhalol-A from brown algae, exhibiting a superior inhibitory effect with p105 (- 7.51kcal/mol) by outperforming PD drugs and anti-inflammatory compounds (- 5.73 to - 4.38kcal/mol). Quantum mechanics and molecular mechanics (QM/MM) calculations and dynamic simulations have confirmed the interactive stability of phlorethopentafuhalol-A with p105. Overall, our combined computational study shows that phlorethopentafuhalol-A derived from brown algae, may have healing properties that could help treat PD.

Near-IR Emissive B-N Lewis Pair-Functionalized Anthracenes via Selective LUMO Extension in Conjugated Dimer and Polymer.

Acenes are attractive as building blocks for low gap organic materials with applications, for example, in organic light emitting diodes, solar cells, bioimaging and diagnostics. Previously, we have shown that modification of dipyridylanthracene via B-N Lewis pair fusion (BDPA) strongly redshifts the emission, while facilitating self-sensitized reactivity toward O2 to reversibly generate the corresponding endoperoxides. Herein, we report on the further expansion of the π-system of BDPA to a vinyl-substituted monomer, vinylene-bridged dimer, and a polymer with an average of 20 chromophores. The extension of π-conjugation results in largely reduced band gaps of 1.8 eV for the dimer and 1.7 eV for the polymer, the latter giving rise to NIR emission with a maximum at 731 nm and an appreciable quantum yield of 7 %. Electrochemical and computational studies reveal efficient delocalization of the lowest unoccupied molecular orbital (LUMO) along the pyridyl-anthracene-pyridyl axis, which results in effective electronic communication between BDPA units, selectively lowers the LUMO, and ultimately narrows the band gap. Time-resolved emission and transient absorption (TA) measurements offer insights into the pertinent photophysical processes. Extension of π-conjugation also slows down the self-sensitized formation of endoperoxides, while significantly accelerating the thermal release of singlet oxygen to regenerate the parent acenes.

Synthesis of β-lactams and transformation to β-amino acid ethyl ester derivatives: Theoretical calculations

Because of the important biological properties of β-amino acids in the present work, two new β-amino acid ethyl ester derivatives were synthesized, and their mechanistic occurrence was investigated. The title compounds were synthesized from related tetralone derivatives containing bromine and methoxy groups. Tetralone derivatives were reduced to their benzyl alcohol derivatives with NaBH4, followed by elimination with p-toluenesulfonic acid (pTSA) to give the desired 1,2-dihydronaphthalene derivatives. The reactions of 1,2-dihydronaphthalenes with chlorosulfonyl isocyanate (CSI) afforded β-lactams. β-Amino acids were obtained from the reaction of β-lactams with EtOH in HCl. Computational studies are concerned with synthesizing four-membered lactams (β-lactam) formed by the reaction between 1,2-dihydronaphthalene derivatives and CSI. The mechanism of the formation of compounds has been elucidated using DFT at M06-2X.

Molecular basis of bacterial lectin recognition of eukaryotic glycans: The case of Mycoplasma pneumoniae and Mycoplasma genitalium cytoadhesins

Mycoplasma pneumoniae and Mycoplasma genitalium are two emerging bacterial pathogens that colonize the human respiratory and urogenital epithelia, respectively. Both pathogens express cell surface cytoadhesins that play a crucial role in the interaction with the host, mediating the attachment to sialylated glycan receptors and triggering infection. The design of competitive binding inhibitors of Mycoplasma cytoadhesins has potential to disrupt these interactions and lessen bacterial pathogenesis. To this end, we report here molecular insights into the adhesion mechanisms of M. pneumoniae and M. genitalium, which are largely mediated by sialylated glycans on the host cell surface. In detail, a combination of Nuclear Magnetic Resonance (NMR) spectroscopy, fluorescence analysis and computational studies allowed us to explore the recognition by the cytoadhesins P40/P90 in M. pneumoniae and P110 in M. genitalium of sialylated N- and O-glycans. We reveal that, unlike other bacterial adhesins, which are characterized by a wide binding pocket, Mycoplasma cytoadhesins principally accommodate the sialic acid residue, in a similar manner to mammalian Siglecs. These findings represent crucial insight into the future development of novel compounds to counteract Mycoplasma infections by inhibiting bacterial adherence to host tissues.

S14-01 Mechanistic insight into the bioactivation of alkylbenzenes from computational studies

S14-01 Mechanistic insight into the bioactivation of alkylbenzenes from computational studies