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At least 145 records · Page 8

Guanosine Dianions Hydrated by One to Four Water Molecules

Intermolecular interactions as those present in molecule…water complexes may profoundly influence the physico-chemical properties of molecules. Here, we carried out an experimentally-computational study on the doubly-deprotonated guanosine monophosphate…water clusters, [dGMP-2H] 2- •nH 2 O (n=1–4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations. Successive addition of water molecules to [dGMP-2H] 2- increases the experimental adiabatic detachment (ADE) and vertical detachment energy (VDE) by 0.5 to 0.1 eV, depending on the cluster size. In order to choose the representative conformations, we combined MD simulations with a clustering procedure to identify low energy geometries for which ADEs and VDEs were computed at the CAM-B3LYP/6-31++G(d,p) level. Our results demonstrate that the assumed approach lead to the sound geometries and energetics of the studied micro-solvates since the calculated ADEs and VDEs are in pretty good agreement with the experimental characteristics. The evolution of hydrogen bonding with cluster size indicates possibility of the occurrence of proton transfer for clusters comprising a larger number of water molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Single Molecule Spectroscopy Studies of Acid–Base Chemical Gradients Using Nile Red as a Probe of Local Surface Acidity

Single molecule spectroscopy studies of local acidity along bifunctional acid-base gradients are reported. Gradients are prepared by directional vapor phase diffusion and subsequent reaction of 3-aminopropyl-trimethoxysilane with a uniform silica film. Gradient formation is confirmed by spectroscopic ellipsometry and by static water contact angle measurements. X-ray photoelectron spectroscopy is used to characterize the nitrogen content and degree of nitrogen protonation along the gradient. Nile Red is employed as the probe dye in single molecule spectroscopy studies of these gradients. While Nile Red is well-known for its solvent sensitivity, it is used here, for the first time, to sense the acid/base properties of the film in two-color wide-field fluorescence imaging experiments. The data reveal broad bimodal distributions of Nile Red emission spectra that vary along the gradient direction. The single-molecule results are consistent with solution-phase ensemble acid/base studies of the dye. The former reveal a gradual transition from a surface dominated by basic aminosilane sites at the high-amine end of the gradient to one dominated by acidic silanol sites at the low-amine end. The sub-diffraction-limited spatial resolution afforded by superlocalization of the single molecules reveals spatial correlations in the acid/base properties of the gradient over ~ 200 nm distances. Furthermore, these studies provide data relevant to the use of aminosilane-modified silica in bifunctional, cooperative chemical catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Recent Advances in Probing Electron Delocalization in Conjugated Molecules by Attached Infrared Reporter Groups for Energy Conversion and Storage

This review article reports an overview of the recent developments in the field of electron delocalization study in organic conjugated molecules by utilizing the vibration frequencies exhibited by the attached functional groups such as nitrile (–C≡N), alkyne (–C≡C–), or carbonyl (–C=O). A brief introduction to electron delocalization, methods for study, and their importance is given first, followed by the application of infrared spectroscopy in organic molecules. Details of molecules with various infrared reporter groups have been explained in respective subsections based on the functional groups. All the reported organic molecules have been structured and presented with the electron delocalization properties studied using an infrared reporter group. Finally, an outlook on this recently promising, exciting, and interesting field of probing electron delocalization using infrared reporter groups is provided.

25 ENERGY STORAGE↗

Triacetic Acid Lactone and 4-Hydroxycoumarin as Bioprivileged Molecules for the Development of Performance-Advantaged Organic Corrosion Inhibitors

Biomass conversion, especially the development of bioprivileged molecules utilizing integration of biological and chemical processes, has shown potential to produce novel chemicals with enhanced properties. Here, organic corrosion inhibitors based on triacetic acid lactone and 4-hydroxycoumarin have been synthesized in good yield and tested for corrosion inhibition on mild steel in both sulfuric acid and hydrochloric acid. Sixteen novel corrosion inhibitors derived from triacetic acid lactone and 4-hydroxycoumarin were efficiently synthesized and twelve of them showed high corrosion inhibition efficiency as confirmed by electrochemical impedance spectroscopy (giving values greater than 78%) and polarization analysis. While triacetic acid lactone-based compounds showed good corrosion inhibition performance, the 4-hydroxycoumarin-based compounds showed further improvement in corrosion inhibition performance. Scanning electron microscopy (SEM) analysis of the mild steel coupon in the presence of selected inhibitors showed that corrosion was significantly diminished, with complementary X-ray photoelectron spectroscopy (XPS) analysis suggesting the inhibitor molecules strongly adsorbed on the steel surface. Quantum chemical calculations showed poor correlation between calculated parameters and the performance of these molecules. This large set of corrosion inhibitors containing a dozen promising corrosion inhibitors is useful for future rational design of corrosion inhibitors. In conclusion, the results demonstrate a new direction for the development of bioprivileged molecules.

09 BIOMASS FUELS↗

Single-Molecule Fluorescence Microscopy Reveals Energy Transfer Active versus Inactive Nanocrystal/Dye Conjugate Pairs

Defect-mediated energy transfer (EnT) is a radiative process that occurs between donor defect states in the forbidden bandgap of semiconductor nanocrystals (NCs) and dye molecules bound to their surfaces. The EnT efficiency depends on the number of dye molecules attached to each NC, the donor–acceptor distance, and the dipole orientation factor between the donor and acceptor, all of which vary across all individual NCs in a sample. While ensemble-level fluorescence spectroscopy measurements have provided average values for donor–acceptor distances, dye-to-NC ratios, and EnT rate constants, questions remain about the impact of donor/acceptor heterogeneity on observed EnT efficiencies. Notably, ensemble-level measurements cannot distinguish between bare NCs and EnT-active versus inactive NC/dye pairs in the same sample batch, limiting the ability to design systems with 100% EnT efficiency. To address this, we studied defect-mediated EnT between AlexaFluor 555 dye acceptors chemically bound to ZnO NC donors at the level of single molecules and single NCs. Interestingly, 20% of bound NC/dye pairs are EnT-inactive, likely contributing to residual defect photoluminescence (PL) observed in ensemble-level measurements and reducing overall EnT efficiency. Single particle-level ZnO defect PL and acceptor fluorescence trajectories exhibited distinct microfluctuations, which are absent in bare ZnO NCs. We hypothesized that our observations can be explained with a competitive dye fluorescence quenching pathway, possibly due to charge transfer between the excited state dye and the ZnO NC. Numerical simulations of single-molecule PL traces for this scenario produced microfluctuations consistent with the experimental results. These findings highlight the impact of sample heterogeneity on EnT processes and provide insights for designing light-harvesting systems with optimized EnT efficiency.

25 ENERGY STORAGE↗

Single-Molecule Charge Transport through Positively Charged Electrostatic Anchors

The charge transport in single-molecule junctions depends critically on the chemical identity of the anchor groups that are used to connect the molecular wires to the electrodes. In this research, we report a new anchoring strategy — called the electrostatic anchor here — formed through the efficient Coulombic interaction between the gold electrodes and the positively charged pyridinium terminal groups. Our results show that these pyridinium groups serve as efficient electrostatic anchors forming robust gold–molecule–gold junctions. Here, we have also observed binary switching in dicationic viologen molecular junctions, demonstrating an electron injection-induced redox switching in single-molecule junctions. We attribute the difference in low- and high conductance states to a dicationic ground state and a radical cationic metastable state, respectively. Overall, this anchoring strategy and redox switching mechanism could constitute the basis for a new class of redox-activated single-molecule switches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Visualizing the Three-Dimensional Arrangement of Hydrogen Atoms in Organic Molecules by Coulomb Explosion Imaging

Structure-sensitive methods based on femtosecond light or electron pulses are now making it possible to measure how molecular structures change during light-induced processes. Despite significant progress, high-fidelity imaging of nuclear positions remains a challenge even for relatively small molecular systems and, notably, regarding the positions of hydrogen atoms. As demonstrated in recent work, X-ray-induced Coulomb explosion imaging (CEI) may overcome this obstacle, as its sensitivity does not depend on the mass of the imaged atoms. The photoinduced ring opening of the heterocyclic molecule 2(5 H )-thiophenone has attracted recent interest. Here, in this work, we show that CEI offers a powerful route to imaging the peripheral H atoms in this molecule and thus, more generally, to tracking detailed nuclear motions (e.g., isomerizations) in organic molecules on ultrafast time scales. Specifically, we record momentum-space Coulomb explosion images that report on the three-dimensional positioning of all nuclei within the molecule, for instance, distinguishing H atoms in C–H bonds that lie within or are directed out of the plane defined by the heavy atoms. The prospect of imaging peripheral H atoms to probe photochemical dynamics is explored by coupling ab initio molecular dynamics with classical Coulomb explosion simulations, thereby differentiating potential photoproduct isomers, including those whose structures primarily differ in the position of the hydrogens.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ab Initio Polariton Spectra of ZnTPP Molecules Collectively Coupled Inside an Optical Cavity

Exciton-polaritons are quasi-particles formed by the quantum mechanical hybridization of electronic and photonic excitations. Despite extensive investigations, a fundamental understanding of molecular polariton spectra and the polariton delocalization from an ab initio theoretical perspective remains elusive. We simulate experimentally measured linear transmission spectroscopy of many Zinc(II) tetraphenylporphyrin (ZnTPP) molecules collectively coupled to a cavity from first principles. Our theoretical approach incorporates many low-lying electronic excitations in ZnTPP molecules, as well as collective light-matter couplings between ZnTPP and the quantized radiation modes, both of which are shown to be the key to accurately recovering the experimental spectra. We further analyzed to what extent the polariton and dark states are delocalized over many molecules, for the first time, using fully ab initio descriptions of the molecules. We finally investigate the line width as a function of detuning, providing new theoretical insights into the experimentally observed motional narrowing behavior. Our work presents first-ofits- kind theoretical studies on molecular polariton spectra, offering a new perspective on molecular polariton formation in realistic ab initio molecular systems whose rich, many-state nature provides spectral features enabled by the high density of electronic states beyond simple quantum optics models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hyperfine and quadrupole interactions for Dy isotopes in DyPc 2 molecules

Nuclear spin levels play a vital role in understanding magnetization dynamics and implementation and control of quantum bits in lanthanide-based single-molecule magnets. We investigate the hyperfine and nuclear quadrupole interactions for 161 Dy and 163 Dy nuclei in anionic DyPc 2 (Pc=phthalocyanine) single-molecule magnets, using multiconfigurational ab initio methods (beyond density-functional theory) including spin–orbit interaction. The two isotopes of Dy are chosen because the others have zero nuclear spin. Both isotopes have the nuclear spin I =5/2, although the magnitude and sign of the nuclear magnetic moment differ from each other. The large energy gap between the electronic ground and first-excited Kramers doublets, allows us to map the microscopic hyperfine and quadrupole interaction Hamiltonian onto an effective Hamiltonian with an electronic pseudo-spin that corresponds to the ground Kramers doublet. Our ab initio calculations illustrate that the coupling between the nuclear spin and electronic orbital angular momentum contributes the most to the hyperfine interaction and that both the hyperfine and nuclear quadrupole interactions for 161 Dy and 163 Dy nuclei are much smaller than those for the 159 Tb nucleus in TbPc 2 single-molecule magnets. The calculated separations of the electronic-nuclear levels are comparable to experimental data reported for 163 DyPc 2 . We demonstrate that hyperfine interaction for the Dy Kramers ion leads to tunnel splitting (or quantum tunneling of magnetization) at zero field. This effect does not occur for TbPc 2 single-molecule magnets. The magnetic field values of the avoided level crossings for 161 DyPc 2 and 163 DyPc 2 are found to be noticeably different, which can be observed from the experiment.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Investigation of the role of hydrogen molecules in 1D simulation of divertor detachment

The role of neutral and charged hydrogenic molecules in detached regimes of tokamak plasmas is investigated using a simplified 1D numerical model. Using MAST Upgrade like conditions, simulations are implemented to study the rollover of target flux Γ in upstream density scan. It is found that if H 2 and H 2 + are considered in simulations a lower target temperature and a larger upstream density will be required to trigger divertor detachment under the same input power and particle flux, and the critical detachment threshold (the critical ratio of upstream static pressure to the power entering the recycling region) is found to be $^{ρ_{up}}_{ρ_{recl}}$ ~ 8.1 NMW -1 at rollover. Molecule–plasma interactions are found to be as crucial as atom–plasma interactions during divertor detachment, both of which account for the majority of plasma momentum loss in the cases studied here. Further analysis of the momentum loss decomposition shows molecule-plasma elastic collisions dominate molecule-plasma interactions, while molecular charge exchange cannot effectively reduce plasma momentum. In terms of H alpha emission, a strong rise of H alpha signal is found to be due to molecular excitation channels when the upstream density further increases after rollover.

SD1D↗

Opportunities for fundamental physics research with radioactive molecules

Molecules containing short-lived, radioactive nuclei are uniquely positioned to enable a wide range of scientific discoveries in the areas of fundamental symmetries, astrophysics, nuclear structure, and chemistry. Recent advances in the ability to create, cool, and control complex molecules down to the quantum level, along with recent and upcoming advances in radioactive species production at several facilities around the world, create a compelling opportunity to coordinate and combine these efforts to bring precision measurement and control to molecules containing extreme nuclei. In this paper, we review the scientific case for studying radioactive molecules, discuss recent atomic, molecular, nuclear, astrophysical, and chemical advances which provide the foundation for their study, describe the facilities where these species are and will be produced, and provide an outlook for the future of this nascent field.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts

The majority of primary and secondary metabolites in nature have yet to be identified, representing a major challenge for metabolomics studies that currently require reference libraries from analyses of authentic compounds. Using currently available analytical methods, complete chemical characterization of metabolomes is infeasible for both technical and economic reasons. For example, unambiguous identification of metabolites is limited by the availability of authentic chemical standards, which, for the majority of molecules, do not exist. Computationally predicted or calculated data are a viable solution to expand the currently limited metabolite reference libraries, if such methods are shown to be sufficiently accurate. For example, determining nuclear magnetic resonance (NMR) spectroscopy spectra in silico has shown promise in the identification and delineation of metabolite structures. Many researchers have been taking advantage of density functional theory (DFT), a computationally inexpensive yet reputable method for the prediction of carbon and proton NMR spectra of metabolites. However, such methods are expected to have some error in predicted 13 >C and 1 H NMR spectra with respect to experimentally measured values. This leads us to the question–what accuracy is required in predicted 13 C and 1 H NMR chemical shifts for confident metabolite identification? Using the set of 11,716 small molecules found in the Human Metabolome Database (HMDB), we simulated both experimental and theoretical NMR chemical shift databases. We investigated the level of accuracy required for identification of metabolites in simulated pure and impure samples by matching predicted chemical shifts to experimental data. We found 90% or more of molecules in simulated pure samples can be successfully identified when errors of 1 H and 13 C chemical shifts in water are below 0.6 and 7.1 ppm, respectively, and below 0.5 and 4.6 ppm in chloroform solvation, respectively. In simulated complex mixtures, as the complexity of the mixture increased, greater accuracy of the calculated chemical shifts was required, as expected. However, if the number of molecules in the mixture is known, e.g., when NMR is combined with MS and sample complexity is low, the likelihood of confident molecular identification increased by 90%.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Identifying Performance Advantaged Biobased Chemicals Utilizing Bioprivileged Molecules

Two technology areas were advanced; a) novel molecules with improved performance in the end use application of organic corrosion inhibitors and flame retardant nylon polymers and b) development of a systematic process for identifying biomass-derived molecules with improved performance in end use applications. In total 17 novel organic corrosion inhibitors were identified that had significantly better performance than the commercial reference organic corrosion inhibitor and 7 novel nylons were synthesized with improved flame retardant properties relative to standard nylon-6,6. While an end-to-end systematic process for identifying biomass-derived molecules with improved end use performance was not completed, important progress was made computational tools for mining chemical structures from the literature and databases as well as establishing reaction network generation algorithms to aid in the discovery of novel molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Statistically-driven Experimental Design to Improve Reference-free Quantification of Small Molecules by Liquid Chromatography-Mass Spectrometry

Non-targeted analysis of small molecules and metabolites in unknown, complex samples using liquid chromatography-tandem mass spectrometry remains challenging. One of the main bottlenecks is the extensive unannotated regions of metabolomics mass spectrometry data, resulting in knowledge gaps. Small molecule annotation in mass spectrometry data has conventionally relied on reference standards and libraries for compound identification and confirmation, which can constrain compound identification to those molecules already known, thus limiting the ability to discover new knowledge and new markers. Retention time prediction can facilitate and expedite unknown compound identification in non-targeted analysis of complex metabolomics samples. Additionally, accurate retention time predictions can also inform sample mixture design for LC-MS/MS analyses. However, current machine learning-based methods for retention time prediction are typically developed for specific chromatographic platforms and are not generalizable across scales. And while technologies and methods to improve reference-free metabolite identification for more comprehensive annotation of unknowns has received much attention, development of the same for quantitation without reference standards has been much more limited, despite its importance in toxicological, environmental, food safety, forensics, and clinical applications. We believe that a reference-free quantitation strategy that exploits mass spectrometry data already collected for reference-free identification can provide much more insight on unknowns, and move the metabolomics field for more complete unknowns characterization. As such, we pursue two efforts to improve upon current state-of-the-art methods in non-targeted analysis: (1) machine learning-based retention time prediction and (2) statistical design of experiments framework for reference-free quantitation. In this work, we develop and demonstrate (1) a generalizable retention time prediction capability across chromatographic conditions and scales, and (2) a statistical design-based framework for response factor contribution elucidation and reference-free quantitation. Evaluation of our retention time prediction model, PrediToR, showed approximately 24% improvement over current models, and we observed approximately 10X improvement in concentration estimation accuracy from our statistical design-based response factor model over a primarily ionization efficiency-based model. We expect that future efforts to improve upon these new capabilities will further advance non-targeted analysis of small molecules towards truly reference-free metabolomics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Laser Spectroscopy of Exotic Atoms and Molecules Containing Octupole-Deformed Nuclei

This project investigated the nuclear, atomic, and molecular structure of exotic atoms and molecules containing actinide isotopes. These short-lived radioactive systems are challenging to produce and study in the laboratory, yet they offer unique opportunities for fundamental science. These nuclei are predicted to exhibit pear-shaped (octupole) deformation, a rare collective nuclear behavior that dramatically enhances their sensitivity to fundamental physics phenomena such as time-reversal- and parity-violating effects. Such enhancements make them ideal probes for exploring open questions in our understanding of the universe such as the origin of the matter–antimatter asymmetry of the universe. To realize these measurements, the project led the development of a new laser spectroscopy experiment at MIT, and later commissioned at the Facility for Rare Isotope Beams (FRIB) at Michigan State University: the Resonance Ionization Spectroscopy Experiment (RISE). RISE combines the spectroscopic precision of collinear laser spectroscopy with the sensitivity of particle-detection techniques, enabling measurements of rare isotopes produced at rates as low as a few ions per second. The beamline was designed, built, and installed, and was successfully commissioned at FRIB during the grant period. RISE is now a permanent capability of the FRIB facility, and has produced several results on the study of rare atoms and molecules for nuclear structure and fundamental symmetries. In parallel with the FRIB program, the project contributed to the first precision laser-spectroscopy measurements of short-lived radioactive molecules. Working with international collaborators at CERN's ISOLDE facility, the team conducted pioneering experiments on radium monofluoride (RaF) and actinium monofluoride (AcF). The results from this work have been published in major journals of science, including Nature, Science, Nature Physics, Nature Communications, and Physical Review Letters. These findings have guided future experiments on the laser cooling of radioactive molecules, opening a new platform for precision tests of fundamental symmetries.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Symmetry‐Breaking Strategy Yields Dopant‐Free Small Molecule Hole Transport Materials for Inorganic Perovskite Solar Cells with 20.58% Efficiency and Outstanding Stability

Abstract Inorganic perovskites are known for their excellent photothermal stability; however, the photothermal stability of all‐inorganic n‐i‐p perovskite solar cells (PSCs) is compromised due to ion diffusion and free radical‐induced degradation caused by the use of doped spiro‐OMeTAD hole transport materials (HTMs). In this study, two isomeric donor–acceptor–donor (D–A–D) type small molecules, namely HBT and HiBT, were developed and used as dopant‐free HTMs, using 2,1,3‐benzothiadiazole or benzo[d][1,2,3]thiadiazole as acceptor moieties. The HiBT molecule, with its symmetry‐breaking features, exhibits a large dipole moment, enhanced coordination‐active sites, and a well‐aligned energy level structure, all of which contribute to passivating perovskite surface defects and improving free charge separation. As a result, inorganic CsPbI 3 PSCs with HiBT HTM achieved an impressive power conversion efficiency (PCE) of 20.58%, the highest reported for dopant‐free HTM‐based inorganic PSCs. Moreover, the enhanced hydrophobic properties of HiBT molecules, coupled with their ability to passivate perovskite surface defects, contribute to significantly improved device stability. The unencapsulated devices based on HiBT HTM retained over 83% and 80% of their initial efficiency after being stored at 85 °C for 50 days and undergoing maximum power point (MPP) tracking at 85 °C for 1100 h, respectively. These results highlight that the symmetry‐breaking strategy is an exceptionally effective approach for designing efficient, dopant‐free small molecule HTMs, significantly contributing to both the high efficiency and enhanced stability of all‐inorganic PSCs.

Chemistry↗

Insights from 20 years of the Molecule of the Month

For 20 years, Molecule of the Month articles have highlighted the functional stories of 3D structures found in the Protein Data Bank (PDB). The PDB is the primary archive of atomic structures of biological molecules, currently providing open access to more than 150,000 structures studied by researchers around the world. The wealth of knowledge embodied in this resource is remarkable, with structures that allow exploration of nearly any biomolecular topic, including the basic science of genetic mechanisms, mechanisms of photosynthesis and bioenergetics, and central biomedical topics like cancer therapy and the fight against infectious disease. The central motivation behind the Molecule of the Month is to provide a user-friendly introduction to this rich body of data, charting a path for users to get started with finding and exploring the many available structures. The Molecule of the Month and related materials are updated regularly at the education portal PDB-101 (http://pdb101.rcsb.org/), offering an ongoing resource for molecular biology educators and students around the world.

59 BASIC BIOLOGICAL SCIENCES↗

Traction-separation response of bilayer graphene interfaces: The role of an intercalated single atomic layer of water molecules and hydroxyl groups

Molecular dynamics simulations of the normal and shear traction-separation response of dry and wet bilayer graphene interfaces were performed. The influence of a single, atomic layer of water molecules sandwiched between graphene layers and hydroxyl functionalization on one or both layers were investigated. Hydroxyl groups provided a shielding effect during normal separation while favoring stick-slip friction under sliding conditions. The single, atomic layer of water molecules confined between hydrophilic and asymmetric hydrophobic/hydrophilic surfaces was found to ease sliding friction. The mechanisms arose from the balance between the attractive and repulsive graphene/water interactions through bridges of single water molecules between the two surfaces and the structure of the water monolayer under confinement for which an out-of-plane water/water hydrogen bond network could not be developed. The single, atomic layer of water molecules reduced the sliding friction the most when both surfaces were hydrophilic and lowered the sliding friction of the asymmetric hydrophobic/hydrophilic interfaces to that when both surfaces were hydrophobic. An optimal hydroxyl surface coverage of less than 10% may exist for efficient water lubrication, with diminishing effect with increasing number of hydroxyl groups. Finally, the findings offer a design strategy for assembling bilayer graphene interfaces with tailored friction and sliding contact properties.

36 MATERIALS SCIENCE↗