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At least 919 records · Page 51

General Protocol for the Accurate Prediction of Molecular 13 C/ 1 H NMR Chemical Shifts via Machine Learning Augmented DFT

An accurate prediction of NMR chemical shifts at affordable computational cost is very important for different types of structural assignments in experimental studies. Density functional theory (DFT) and gauge-including atomic orbital (GIAO) are two of the most popular computational methods for NMR calculation, yet they often fail to resolve ambiguities in structural assignments. In this work, we present a new method that uses machine learning (ML) techniques (DFT + ML) that significantly increases the accuracy of 13 C/ 1 H NMR chemical shift prediction for a variety of organic molecules. The input of the generalizable DFT + ML model contains two critical parts: one is a vector providing insights into chemical environments, which can be evaluated without knowing the exact geometry of the molecule; the other one is the DFT-calculated isotropic shielding constant. The DFT + ML model was trained with a data set containing 476 13 C and 270 1 H experimental chemical shifts. For the DFT methods used here, the root mean square deviations (RMSDs) for the errors between predicted and experimental 13 C/ 1 H chemical shifts can be as small as 2.10/0.18 ppm, which is much lower than those from simple DFT (5.54/0.25 ppm), or DFT + linear regression (LR) (4.77/0.23 ppm) approaches. It also has a smaller maximum absolute error than two previously proposed NMR-predicting ML models. The robustness of the DFT + ML model is tested on two classes of organic molecules (TIC10 and hyacinthacines), where the correct isomers were unambiguously assigned to the experimental ones. Overall, the DFT + ML model shows promise for structural assignments in a variety of systems, including stereoisomers, that are often challenging to determine experimentally.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models

Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, natural population analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree–Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 Å of the central water) in the quantum chemical calculation converges the charges of the central water molecule. Furthermore, our final pragmatic quantum chemical charge-assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 Å.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enhanced detection of volatile organic compounds (VOCs) by caffeine modified carbon nanotube junctions

Detection of vapor phase analytes and gas molecules is primarily essential for numerous applications including medical diagnostic, environmental monitoring, chemical threat detection, food quality control, and chemical warfare agents. Here, we developed Caffeine functionalized carbon nanotubes (CNTs) random network based vapor quantum resistive sensors (vQRSs) for volatile organic compounds (VOCs) detection. The localized transmission electron microscopy (TEM) image and energy dispersive X-ray spectroscopy (EDS) confirm migration of caffeine to CNT–CNT junction (CNTj). We have recorded more than one order of magnitude higher sensitivity and unique selectivity towards selective VOCs (e.g., acetone, toluene, ethanol, methanol, etc.) with short response time (few seconds) for caffeine modified CNT junction (Caf-CNTj) vQRSs. Molecular dynamics (MD) calculations suggest that the sensitivity of the sensor is diffusion limited, with an advective contribution for ethanol. Furthermore, the designed Caf-CNTj sensors can potentially be important candidate to be a part of electronic nose used for various application such as breath analysis and food quality monitoring.

36 MATERIALS SCIENCE↗

NEXAFS spectroscopy of alkylated benzothienobenzothiophene thin films at the carbon and sulfur K-edges

Alkylated benzothienobenzothiophenes are an important class of organic semiconductors that exhibit high performance in solution-processed organic field-effect transistors. In this work, we study the near-edge x-ray absorption fine-structure (NEXAFS) spectra of 2,7-didecyl[1]benzothieno[3,2-b][1]benzothiophene (C 10 -BTBT) at both the carbon and sulfur K-edges. Angle-resolved experiments of thin films are performed to characterize the dichroism associated with molecular orientation. First-principles calculations using the density functional theory-based many-body x-ray absorption spectroscopy (MBXAS) method are also performed to correlate the peaks observed and their dichroism with transitions to specific antibonding molecular orbitals. Interestingly, the dichroism of the dominant, lowest energy peak is opposite at the carbon and sulfur K-edges. While the low-energy peak at the carbon K-edge is assigned to carbon 1s → π* transitions with transition dipole moment (TDM) perpendicular to the planar BTBT core, the dominant low energy peak at the sulfur K-edge is assigned to sulfur 1s → σ* transitions with TDM oriented along the long axis of the BTBT core. These differences at the sulfur and carbon K-edges are understood through the MBAXS simulations that find a reordering of the energy of the lowest energy π* and σ* transitions at the sulfur K-edge due to the strong localization of the σ* orbital over the sulfur atom. This work highlights differences in the NEXAFS spectra of organic semiconductors at carbon and sulfur K-edges and provides new insights into peak assignment and x-ray dichroism relevant for studying the molecular orientation of organic semiconductor films.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Self-Consistent Field Methods for Excited States in Strong Magnetic Fields: A Comparison Between Energy - and Variance-based Approaches

An efficient implementation of geometrical derivatives at the Hartree–Fock (HF) and current-density functional theory (CDFT) levels is presented for the study of molecular structure in strong magnetic fields. The required integral derivatives are constructed using a hybrid McMurchie–Davidson and Rys quadrature approach, which combines the amenability of the former to the evaluation of derivative integrals with the efficiency of the latter for basis sets with high angular momentum. In addition to its application to evaluating derivatives of four-center integrals, this approach is also applied to gradients using the resolution-of-the-identity approximation, enabling efficient optimization of molecular structure for many-electron systems under a strong magnetic field. The CDFT contributions have been implemented for a wide range of density functionals up to and including the meta-GGA level with current-density dependent contributions and (range-separated) hybrids for the first time. Illustrative applications are presented to the OH and benzene molecules, revealing the rich and complex chemistry induced by the presence of an external magnetic field. Challenges for geometry optimization in strong fields are highlighted, along with the requirement for careful analysis of the resulting electronic structure at each stationary point. The importance of correlation effects is examined by comparison of results at the HF and CDFT levels. The present implementation of molecular gradients at the CDFT level provides a cost-effective approach to the study of molecular structure under strong magnetic fields, opening up many new possibilities for the study of chemistry in this regime.

Comparison↗

Accurate Thermochemistry of Complex Lignin Structures via Density Functional Theory, Group Additivity, and Machine Learning

A molecular-level understanding of lignin structures and bond dissociation energies could facilitate depolymerization technologies. Still, this information is currently limited due to the lack of databases and the simplification of surrogate models. Here, substitution effects on seven common linkages in lignin polymers are systematically investigated. An automated reaction network generator is employed to create a database of structures. A new group additivity (GA) model based on principal component analysis (PCA) descriptors is introduced and trained on gas-phase density functional theory data of 4100 species at the M06-2X/6-311++G(d,p) level. Hydrogen bonds, local steric, and nonaromatic ring contributions are also incorporated. Lastly, we improve the accuracy of the group additivity model to reach the G4 theory by computing a data set of 770 species at this level and using a data fusion approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spectral scheme for atomic structure calculations in density functional theory

In this study, we present a spectral scheme for atomic structure calculations in pseudopotential Kohn-Sham density functional theory. In particular, after applying an exponential transformation of the radial coordinates, we employ global polynomial interpolation on a Chebyshev grid, with derivative operators approximated using the Chebyshev differentiation matrix, and integrations using Clenshaw-Curtis quadrature. We demonstrate the accuracy and efficiency of the scheme through spin-polarized and unpolarized calculations for representative atoms, while considering local, semilocal, and hybrid exchange-correlation functionals. In particular, we find that $\mathcal{O}$(200) grid points are sufficient to achieve an accuracy of 1 microhartree in the eigenvalues for optimized norm conserving Vanderbilt pseudopotentials spanning the periodic table from atomic number Ζ = 1 to 83.

74 ATOMIC AND MOLECULAR PHYSICS↗

Decoding polymer self-dynamics using a two-step approach

The self-correlation function and corresponding self-intermediate scattering function in Fourier space are important quantities for describing the molecular motions of liquids. This work draws attention to a largely overlooked issue concerning the analysis of these space-time density-density correlation functions of polymers. Here, we show that the interpretation of non-Gaussian behavior of polymers is generally complicated by intrachain averaging of distinct self-dynamics of different segments. By the very nature of the mathematics involved, the averaging process not only conceals critical dynamical information, but also contributes to the observed non-Gaussian dynamics. To fully expose this issue and provide a thorough benchmark of polymer self-dynamics, we perform analyses of coarse-grained molecular dynamics simulations of linear and ring polymer melts as well as several theoretical models using a “two-step” approach, where interchain and intrachain averagings of segmental self-dynamics are separated. While past investigations primarily focused on the average behavior, our results indicate that a more nuanced approach to polymer self-dynamics is clearly required.

36 MATERIALS SCIENCE↗

The Atomic Drill Bit: Precision Controlled Atomic Fabrication of 2D Materials

The ability to deterministically fabricate nanoscale architectures with atomic precision is the central goal of nanotechnology, whereby highly localized changes in the atomic structure can be exploited to control device properties at their fundamental physical limit. Here, an automated, feedback-controlled atomic fabrication method is reported and the formation of 1D–2D heterostructures in MoS 2 is demonstrated through selective transformations along specific crystallographic orientations. The atomic-scale probe of an aberration-corrected scanning transmission electron microscope (STEM) is used, and the shape and symmetry of the scan pathway relative to the sample orientation are controlled. The focused and shaped electron beam is used to reliably create Mo 6 S 6 nanowire (MoS-NW) terminated metallic-semiconductor 1D–2D edge structures within a pristine MoS 2 monolayer with atomic precision. From these results, it is found that a triangular beam path aligned along the zig-zag sulfur terminated (ZZS) direction forms stable MoS-NW edge structures with the highest degree of fidelity without resulting in disordering of the surrounding MoS 2 monolayer. Density functional theory (DFT) calculations and ab initio molecular dynamic simulations (AIMD) are used to calculate the energetic barriers for the most stable atomic edge structures and atomic transformation pathways. These discoveries provide an automated method to improve understanding of atomic-scale transformations while opening a pathway toward more precise atomic-scale engineering of materials.

2D materials↗

Multiscale and Multimodal Characterization of 2D Titanium Carbonitride MXene

Here, a comprehensive study on the prototype solid solution phase carbonitride MXene Ti 3 CN is conducted using nuclear magnetic resonance, electron spin resonance, total and quasi-elastic neutron scattering, combined with density functional theory-based electronic structure and molecular dynamic calculations. The combination of experiment and theory lead toward rational atomic structural models of Ti 3 CN. The remnant Al ions from the etching process significantly tune the interlayer spacing, distinct from the more typical MXene, Ti 3 C 2 , prepared similarly. Neutron scattering indicates the surface terminations of Ti 3 CN display high oxygen and fluorine concentrations and rather low hydroxyl and hydrogen concentrations. Calculations show that the structure including both the residual Al ions and mixed surface terminations give the best agreement with the measurements. The water molecules in Ti 3 CN are highly immobile, in strong contrast to those in Ti 3 C 2 . The analysis of the electronic structure suggests that the nitride MXene displays higher conductivity than the carbides. Finally, the absence of hydroxyl groups in terminations, the solid-solution in the anion sites, the remnants within layers, and immobile water altogether make the carbonitrides a unique series in the MXene family, implying a further exploration of their exotic properties and applications in energy storage.

36 MATERIALS SCIENCE↗

Impact of Halogen Groups on the Properties of PEA–Based 2D Pb–Sn Halide Perovskites

Tuning broad emission in 2D Pb–Sn halide perovskites (HPs) is essential for advancing optoelectronic applications, particularly for color-tunable and white-light-emitting devices. This broad emission is linked to structural factors, such as defects and phase segregation of the Pb component within the Pb–Sn system, which are strongly influenced by the molecular structure and chemical properties of spacer cations. Atomic tuning of the spacers via halogenation opens up a new way to fine-tune the molecular properties, enabling further augmentations of HP functionalities. Nevertheless, the distinct broad emission's sensitivity to spacer chemistry remains underexplored. Here, halogenation's influence is systematically investigated on 2D HP emission characteristics using a high-throughput workflow. These findings reveal that the F-containing phenethylammonium (4F-PEA) spacer narrows the broadband PL, whereas Cl broadens it. Through a correlative study, it is found that 4F-PEA reduces not only the local phase segregation but also the defect levels and microstrains in 2D HPs. This is likely attributed to the manifestation of less lattice distortion via stronger surface coordination of the dipole-augmented 4F-PEA. Furthermore, these results highlight halogenation as a key factor in modulating phase segregation and defect density in 2D Pb–Sn HPs, offering a promising pathway to tune the emission for enhanced optoelectronic performance.

2D Pb-Sn halide perovskites↗

Heterotrimetallic Mixed‐Valent Molecular Precursors Containing Periodic Table Neighbors: Assignment of Metal Positions and Oxidation States

Abstract A known trinuclear structure was used to design the heterobimetallic mixed‐valent, mixed‐ligand molecule [Co II (hfac) 3 −Na−Co III (acac) 3 ] ( 1 ). This was used as a template structure to develop heterotrimetallic molecules [Co II (hfac) 3 −Na−Fe III (acac) 3 ] ( 2 ) and [Ni II (hfac) 3 −Na−Co III (acac) 3 ] ( 3 ) via isovalent site‐specific substitution at either of the cobalt positions. Diffraction methods, synchrotron resonant diffraction, and multiple‐wavelength anomalous diffraction were applied beyond simple structural investigation to provide an unambiguous assignment of the positions and oxidation states for the periodic table neighbors in the heterometallic assemblies. Molecules of 2 and 3 are true heterotrimetallic rather than a statistical mixture of two heterobimetallic counterparts. Trinuclear platform 1 exhibits flexibility in accommodating a variety of di‐ and trivalent metals, which can be further utilized in the design of molecular precursors for the NaMM′O 4 functional oxide materials.

Han, Haixiang↗

Aqueous Phase Aldol Condensation of Formaldehyde and Acetone on Anatase TiO2(101) Surface: A Theoretical Investigation

A mechanistic understanding of catalytic reactions at solid-liquid interface is limited both experimentally and theoretically but attracts much interest. Using density functional theory calculations (DFT) and ab initio molecular dynamics (AIMD) simulations, we investigated the effect of liquid water on a-H abstraction, C-C coupling, and dehydration steps of aldol condensation of formaldehyde and acetone on an anatase TiO2(101) surface. The existence of the aqueous phase lowered the Gibbs energy of activation of dehydration step pronouncedly from 187 to 74 kJ/mol through proton transfer mechanism, making the hydrogenation pathway more favorable in the aqueous phase. In contrast, a mixed route prevails in the vapor phase. This work provides insights into the effect of the bulk water through a proton transfer mechanism on the dehydrogenation, C-C coupling, and dehydration

anatase TiO2, formaldehyde and acetone, aldol cond↗

Speciation and diffusive dynamics in hydrated grain boundaries of complex oxide Gd2Ti2O7

Abstract Grain boundaries in polycrystalline materials significantly affect their properties, such as ionic transport, corrosion, and chemical durability. The pyrochlore compound (Gd 2 Ti 2 O 7 ) is employed as a model for complex oxides and is known for its diverse applications, including nuclear waste immobilization. Density functional theory-based first-principles molecular dynamics simulations were performed at different temperatures on the hydrated grain boundary system. The results show extensive transformations within the grain boundaries among hydrous water species (OH − , H 2 O, and H 3 O + ). The temperature dependence of self-diffusion coefficients follows Arrhenius behavior, with an activation energy of 35.9 kJ/mol for hydrogen and 46.3 kJ/mol for oxygen. The lifetime of OH − is about three to four times longer than that of H 2 O at temperatures from 800 to 2100 K, suggesting the greater stability of OH − over H 2 O, a unique characteristic of the grain boundaries. The estimated lifetime of the hydrous species decreases as the temperature increases, with an activation energy of 9.9 kJ/mol for OH − and 13.4 kJ/mol for H 2 O. While Gd 3 + is more mobile than Ti 4+ , both the Gd 3 + and Ti 4+ cations are orders of magnitude less mobile than the water species. The results suggest that water species are much more mobile within grain boundaries than in the bulk crystal and have the potential to penetrate deep into polycrystalline materials through grain boundaries, leading to grain boundary degradation and dissolution. The different mobilities of cations in complex oxides can lead to leaching of certain cations and incongruent dissolution during the chemical weathering of Earth and industrial materials.

B. Ghosh, Dipta↗

Protein–protein interactions between tenascin-R and RPTPζ/phosphacan are critical to maintain the architecture of perineuronal nets

Neural plasticity, the ability to alter the structure and function of neural circuits, varies throughout the age of an individual. The end of the hyperplastic period in the central nervous system coincides with the appearance of honeycomb-like structures called perineuronal nets (PNNs) that surround a subset of neurons. PNNs are a condensed form of neural extracellular matrix that include the glycosaminoglycan hyaluronan and extracellular matrix proteins such as aggrecan and tenascin-R (TNR). PNNs are key regulators of developmental neural plasticity and cognitive functions, yet our current understanding of the molecular interactions that help assemble them remains limited. Disruption of Ptprz1, the gene encoding the receptor protein tyrosine phosphatase RPTPζ, altered the appearance of nets from a reticulated structure to puncta on the surface of cortical neuron bodies in adult mice. The structural alterations mirror those found in Tnr -/- mice, and TNR is absent from the net structures that form in dissociated cultures of Ptprz1 -/- cortical neurons. These findings raised the possibility that TNR and RPTPζ cooperate to promote the assembly of PNNs. Here, we show that TNR associates with the RPTPζ ectodomain and provide a structural basis for these interactions. Furthermore, we show that RPTPζ forms an identical complex with tenascin-C, a homolog of TNR that also regulates neural plasticity. Finally, we demonstrate that mutating residues at the RPTPζ–TNR interface impairs the formation of PNNs in dissociated neuronal cultures. Overall, this work sets the stage for analyzing the roles of protein–protein interactions that underpin the formation of nets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Accounting for Sustainability and Performance: Contrasting Effects of PET-Derived Modifiers on Asphalt Durability

The valorization of waste plastics in roadway infrastructure requires careful balance between sustainability and performance, as ineffective modifiers may incur both environmental and financial costs. This study shows that two modifiers derived from the same waste plastic source (PET)-DOTP (N1,N4-(dioctyl)terephthalamide) and HETP (N1,N4-Bis(2-hydroxyethyl)terephthalamide)-exhibit opposite effects on asphalt properties, despite having nearly the same carbon footprint. DOTP improves elastic recovery in multiple creep recovery tests (MCRT), while HETP increases strain accumulation and reduces elasticity. Density functional theory (DFT) shows that DOTP's molecular structure can disperse well in bitumen mixtures by binding to both polar and non-polar components. In contrast, HETP binds only to the binder's polar sites, lacking adequate dispersion. This increases the risk of aggregation of polar compounds in the bitumen mixture, resulting in a more deformation-prone binder. A techno-economic analysis highlights trade-offs between sustainability and performance in industrial-scale synthesis. This study advocates for applying first-principles thinking in material design, coupled with experimental validation, to engineer plastic waste-derived additives that achieve both performance and sustainability goals.

36 MATERIALS SCIENCE↗

Simplifying computational workflows with the Multiscale Atomic Zeolite Simulation Environment (MAZE)

Zeolites, an important class of 3-dimensional nanoporous materials, have been widely explored for a variety of applications including gas storage, separations, and catalysis. As the properties of these aluminosilicate materials depend on a number of factors (e.g., framework topology, Si/Al ratio, extra-framework cations etc.), detailed experiments (e.g., catalytic properties, adsorption capacities etc.) are often limited to only a handful of materials. Computational methods have played an important role in (1) providing molecular level insights to rationalize experimental observations, and (2) screening large libraries of zeolites to identify promising candidates for experimental synthesis and validation. Different levels of theory and computational chemistry codes are necessary to describe the range of relevant phenomena such as adsorption (e.g., grand canonical Monte Carlo), diffusion (e.g., molecular dynamics), and chemical reactions (e.g., density functional theory). Manipulation of atomic structures, handling of input files, and developing robust workflows becomes quite cumbersome. To mitigate these challenges, we describe the development of the Multiscale Atomic Zeolite Simulation Environment (MAZE) – a Python package that simplifies zeolite-specific calculation workflows by providing a user-friendly interface for systematically manipulating zeolite structures

97 MATHEMATICS AND COMPUTING↗