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We report QDπ-v1.0 for modeling the internal energy of drug molecules containing H, C, N, and O atoms. The QDπ model is in the form of a quantum mechanical/machine learning potential correction (QM/Δ-MLP) that uses a fast third order self-consistent density-functional tight-binding (DFTB3/ 3OB) model that is corrected to a quantitatively high-level of accuracy through a deep-learning potential (DeepPot-SE). The model has the advantage that it is able to properly treat electrostatic interactions and handle changes in charge/protonation states. The model is trained against reference data computed at the ωB97X/6-31G* level (as in the ANI-1x data set) and compared to several other approximate semiempirical and machine learning potentials (ANI-1x, ANI-2x, DFTB3, MNDO/d, AM1, PM6, GFN1-xTB, and GFN2-xTB). The QDπ model is demonstrated to be accurate for a wide range of intra-and intermolecular interactions (despite its intended use as an internal energy model) and has shown to perform exceptionally well for relative protonation/deprotonation energies and tautomers. An example application to model reactions involved in RNA strand cleavage catalyzed by protein and nucleic acid enzymes illustrates QDπ has average errors less than 0.5 kcal/mol, whereas the other models compared have errors over an order of magnitude greater. Taken together, this makes QDπ highly attractive as a potential force field model for drug discovery., This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Theory and Computation, copyright © 2023 American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jctc.2c01172

Understanding hydrogen-metal interactions is important in various fields of surface science, including the aqueous corrosion of metals. The interaction between atomic H and a Mg surface is a key process for the formation of sub-surface Mg hydride, which may play an important role in Mg aqueous corrosion. In the present work, we performed first-principles Density Functional Theory (DFT) calculations to study the mechanisms for hydrogen adsorption and crystalline Mg hydride formation under aqueous conditions. The Electron Localisation Function (ELF) is found to be a promising indicator for predicting stable H adsorption in the Mg surface. It is found that H adsorption and hydride layer formation is dominated by high ELF adsorption sites. Our calculations suggest that the on-surface adsorption of atomic H, OH radicals and atomic O could enhance the electron localisation at specific sites in the sub-surface region, thus forming effective H traps locally. This is predicted to result in the formation of a thermodynamically stable sub-surface hydride layer, which is a potential precursor of the crucial hydride corrosion product of magnesium.

To advance the understanding of the degradation of the liquid electrolyte and Si electrode, and their interface, we exploit the latest developments in cryo-atom probe tomography. We evidence Si anode corrosion from the decomposition of the Li salt before charge-discharge cycles even begin. Volume shrinkage during delithiation leads to the development of nanograins from recrystallization in regions left amorphous by the lithiation. The newly created grain boundaries facilitate pulverization of nanoscale Si fragments, and one is found floating in the electrolyte. P is segregated to these grain boundaries, which confirms the decomposition of the electrolyte. As structural defects are bound to assist the nucleation of Li-rich phases in subsequent lithiations and accelerate the electrolyte's decomposition, these insights into the developed nanoscale microstructure interacting with the electrolyte contribute to understanding the self-catalyzed/accelerated degradation Si anodes and can inform new battery designs unaffected by these life-limiting factors.

Hyperpolarization using signal amplification by reversible exchange (SABRE) relies on target molecules and parahydrogen coordinating to a transition metal catalyst. Identification of this coordinated state becomes increasingly important, especially since bio-relevant targets such as pyruvate and amino acids exhibiting multiple binding sites are becoming compatible with SABRE. In this report, we present a fingerprinting method to discriminate and identify ligand binding sites without requiring the presence of a sensitive or isotope-labeled heteroatom. Adding a small concentration of protons to a deuterated medium, spontaneous 1H/D scrambling of exchangeable protons encodes the ligands each with an isotopological fingerprint. By use of rapid 2D zero quantum NMR, the binding sites are decoded from the hydrides in less than a minute. The new methodology is explained and demonstrated on Ir mixed complexes with pyridine, benzylamine, and ammonia as common N-functional ligands. ispartof: Journal Of Physical Chemistry Letters vol:13 issue:15 pages:3516-3522 ispartof: location:United States status: published

An active environment is any atomic or molecular system changing a chromophore's nonadiabatic dynamics compared to the isolated molecule. The action of the environment on the chromophore occurs by changing the potential energy landscape and triggering new energy and charge flows unavailable in the vacuum. Surface hopping is a mixed quantum-classical approach whose extreme flexibility has made it the primary platform for implementing novel methodologies to investigate the nonadiabatic dynamics of a chromophore in active environments. This Perspective paper surveys the latest developments in the field, focusing on charge and energy transfer processes. ispartof: PHYSICAL CHEMISTRY CHEMICAL PHYSICS vol:25 issue:12 pages:8293-8316 ispartof: location:England status: published

Rate coefficients for the reaction of CN with CH2O were measured for the first time below room temperature in the range 32-103 K using a pulsed Laval nozzle apparatus together with the Pulsed Laser Photolysis-Laser-Induced Fluorescence technique. The rate coefficients exhibited a strong negative temperature dependence, reaching (4.62 ± 0.84) × 10-11 cm3 molecule-1 s-1 at 32 K, and no pressure dependence was observed at 70 K. The potential energy surface (PES) of the CN + CH2O reaction was calculated at the CCSD(T)/aug-cc-pVTZ//M06-2X/aug-cc-pVTZ level of theory, with the lowest energy channel to reaction characterized by the formation of a weakly-bound van der Waals complex, bound by 13.3 kJ mol-1, prior to two transition states with energies of -0.62 and 3.97 kJ mol-1, leading to the products HCN + HCO or HNC + HCO, respectively. For the formation of formyl cyanide, HCOCN, a large activation barrier of 32.9 kJ mol-1 was calculated. Reaction rate theory calculations were performed with the MESMER (Master Equation Solver for Multi Energy well Reactions) package on this PES to calculate rate coefficients. While this ab initio description provided good agreement with the low-temperature rate coefficients, it was not capable of describing the high-temperature experimental rate coefficients from the literature. However, increasing the energies and imaginary frequencies of both transition states allowed MESMER simulations of the rate coefficients to be in good agreement with data spanning 32-769 K. The mechanism for the reaction is the formation of a weakly-bound complex followed by quantum mechanical tunnelling through the small barrier to form HCN + HCO products. MESMER calculations showed that channel generating HNC is not important. MESMER simulated the rate coefficients from 4-1000 K which were used to recommend best-fit modified Arrhenius expressions for use in astrochemical modelling. The UMIST Rate12 (UDfa) model yielded no significant changes in the abundances of HCN, HNC, and HCO for a variety of environments upon inclusion of rate coefficients reported here. The main implication from this study is that the title reaction is not a primary formation route to the interstellar molecule formyl cyanide, HCOCN, as currently implemented in the KIDA astrochemical model. ispartof: PHYSICAL CHEMISTRY CHEMICAL PHYSICS vol:25 issue:11 pages:7719-7733 ispartof: location:England status: published

We investigate the phase behavior of model ternary triacylglycerol blends, comprising triolein (C57H104O6, OOO), tripalmitin (C51H98O6, PPP) and tristearin (C57H110O6, SSS), building upon extensive characterisation of single and binary mixtures, in order to rigorously map the thermal transitions of model natural ‘fats’. A combination of calorimetry, X-ray diffraction, and FTIR spectroscopy is employed to determine crystallisation and melting temperatures and identify the corresponding phases in the complex ternary system. We recover the eutectic behaviour of SSS-PPP blends and the invariability of OOO neat transitions, and resolve the complex β′ + β ternary surface, reflecting the roles of unsaturation and polymorphism of its constituents. Our results provide a representation of the OOO:PPP:SSS:temperature phase behaviour into a triangular prism, consistent with binary pair-wise data, which can inform a range of food science, cosmetic, pharmaceutical and cleaning applications that depend strongly on the physical-chemistry of such multicomponent ‘triglycerides’.

In this work, we develop a photocatalyst wherein nitrogen and phosphorus co-doped carbon quantum dots are scaffolded onto TiO2 nanoparticles (NPCQD/TiO2), denoted as NPCT hereafter. The developed NPCT photocatalyst exhibits an enhanced visible light photocatalytic hydrogen production of 533 μmol h−1 g−1 compared to nitrogen doped CQD/TiO2 (478 μmol h−1 g−1), phosphorus doped CQD/TiO2 (451 μmol h−1 g−1) and pure CQD/TiO2 (427 μmol h−1 g−1) photocatalysts. The enhanced photocatalytic activity of the NPCT photocatalyst is attributed to the excellent synergy between NPCQDs and TiO2 nanoparticles, which results in the creation of virtual energy levels, a decrease in work function and suppressed recombination rates, thereby increasing the lifetime of photogenerated electrons. A detailed mechanism is proposed for the enhancement in visible light hydrogen production by the NPCT photocatalyst from the experimental results, Mott–Schottky plots and ultraviolet photoelectron spectroscopy results. Further, first-principles density functional theory (DFT) simulations are carried out which predict the decrease in the work function and band gap, and the increase in the density of states of NPCT as the factors responsible for the observed enhancement in visible light photocatalytic hydrogen production.

Sunlight is an abundant and clean energy source, the harvesting of which could make a significant contribution to society's increasing energy demands. Metal halide perovskites (MHP) have recently received attention for solar fuel generation through photocatalysis and solar-driven electrocatalysis. However, MHP photocatalysis is limited by low solar energy conversion efficiency, poor stability, and impractical reaction conditions. Compared to photocatalysis, MHP solar-driven electrocatalysis not only exhibits higher solar conversion efficiency but also is more stable when operating under practical reaction conditions. In this Perspective, we outline three leading types of MHP solar-driven electrocatalysis device technologies now in the research spotlight, namely, (1) photovoltaic-electrochemical (PV-EC), (2) photovoltaic-photoelectrochemical (PV-PEC), and (3) photoelectrochemical (PEC) approaches for solar-to-fuel reactions, including water-splitting and the CO2 reduction reaction. In addition, we compare each technology to show their relative technical advantages and limitations and highlight promising research directions for the rapidly emerging scientific field of MHP-based solar-driven electrocatalysis. ispartof: JOURNAL OF PHYSICAL CHEMISTRY LETTERS vol:13 issue:1 pages:25-41 ispartof: location:United States status: published

In this paper, a 40 GHz wavelength division multiplexing communication system-based optical frequency comb generator (WDM–OFCG) is design and investigated via OptiSystem software. The proposed design produced up to 25 channels with constant channel spacing of 40 GHz and average power of –10.84 dBm. The generated comb is spread over approximately 8 nm, ranging from 1546.17 to 1553.85 nm. In addition, the generated comb is employed as a multiwavelength laser source to carry information with a bit rate of 375 Gbps over a 120 km link distance. This represents an efficient evaluation to the proposed design since the achievable bit rate product repeater distance (BL) is about 45,000 (Gbps.km).

We describe the generalized weighted thermodynamic perturbation (gwTP) method for estimating the free energy surface of an expensive "high-level" potential energy function from the umbrella sampling performed with multiple inexpensive "low-level" reference potentials. The gwTP method is a generalization of the weighted thermodynamic perturbation (wTP) method developed by Li and co-workers [J. Chem. Theory Comput. 2018, 14, 5583-5596] that uses a single "low-level" reference potential. The gwTP method offers new possibilities in model design whereby the sampling generated from several low-level potentials may be combined (e.g., specific reaction parameter models that might have variable accuracy at different stages of a multistep reaction). The gwTP method is especially well suited for use with machine learning potentials (MLPs) that are trained against computationally expensive ab initio quantum mechanical/molecular mechanical (QM/MM) energies and forces using active learning procedures that naturally produce multiple distinct neural network potentials. Simulations can be performed with greater sampling using the fast MLPs and then corrected to the ab initio level using gwTP. The capabilities of the gwTP method are demonstrated by creating reference potentials based on the MNDO/d and DFTB2/MIO semiempirical models supplemented with the "range-corrected deep potential" (DPRc). The DPRc parameters are trained to ab initio QM/MM data, and the potentials are used to calculate the free energy surface of stepwise mechanisms for nonenzymatic RNA 2'-O-transesterification model reactions. The extended sampling made possible by the reference potentials allows one to identify unequilibrated portions of the simulations that are not always evident from the short time scale commonly used with ab initio QM/MM potentials. We show that the reference potential approach can yield more accurate ab initio free energy predictions than the wTP method or what can be reasonably afforded from explicit ab initio QM/MM sampling., This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Theory and Computation, copyright © 2022 American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jpca.2c06201

Purpose The purpose of this study is to investigate the ammonia sensing performance of polyaniline/polyethylene oxide (PANI/PEO) and polyaniline/polyethylene oxide/zinc oxide (PANI/PEO-ZnO) composite nanofibers at room temperature. Design/methodology/approach Gas sensor structures were fabricated using micro-fabrication techniques. First, onto the SiO2 wafer, gold electrodes were fabricated via thermal evaporation. PANI/PEO nanofibers were produced by the electrospinning method and the ZnO layer was deposited by RF magnetron sputtering on the electrospun nanofibers as a sensing layer. Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) were performed for characterization analysis of nanofibers. After all, gas sensing analysis of PANI/PEO and PANI/PEO/ZnO nanofibers was performed using an experimental setup at room temperature conditions. Findings FTIR analysis confirms the presence of functional groups of PANI, PEO and ZnO in nanofiber structure. SEM images demonstrate beads-free, thinner and smooth nanofibers with ZnO contribution to electrospun PANI/PEO nanofibers. Moreover, according to the gas sensing results, the PANI/PEO nanofibers exhibit 115 and 457 s response time and recovery time, respectively. However, the PANI/PEO/ZnO nanofibers exhibit 245 and 153 s response time and recovery time, respectively. Originality/value In this study, ZnO was deposited via RF magnetron sputtering techniques on PANI/PEO nanofibers as a different approach instead of in situ polymerization, to investigate and enhance the sensor response and recovery time of the PANI/PEO/ZnO and PANI/PEO composite nanofibers to ammonia. These results indicated that ZnO can enhance the sensing properties of conductive polymer based resistive sensors.

Medicinal plants have been used throughout history in the treatment of many diseases in traditional Anatolian folk medicine as well as all over the world. The rapid increase in agricultural and industrial activities due to the increasing population around the world causes air, water and soil pollution, and accumulation of potentially toxic elements in medicinal plants. In this study, plant mineral nutrients and potentially toxic elements analyzes were carried out in 38 plant species belonging to the medicinally important families Asteraceae, Fabaceae and Lamiaceae. The percentage of macroelements (in %) varies between 0.20 and 1.46 for calcium, 0.08 and 1.35 for potassium, 0.04 and 0.24 for magnesium, 0.01 and 0.34 for sodium, while concentrations of microelements and potentially toxic elements (in mg kg−1) vary between 3.21 and 721.28 for aluminum, 41.33 and 231.01 for boron, 0.01 and 0.61 for cadmium, 1.09 and 47.79 for chromium, 12.90 and 43.13 for copper, 17.75 and 1109.39 for iron, 51.50 and 715.48 for manganese, 0.12 and 9.42 for nickel, 1.58 and 22.11 for lead and finally 80.82 and 260.08 for zinc. In addition, estimated daily intake (EDI), target hazard quotient (THQ), and hazard index (HI) for potentially toxic elements, and Recommended Dietary Allowance (RDA) values for mineral nutrients were calculated. In some samples in industrial and mining areas, accumulation of some potentially toxic elements was slightly above the permissible limits set by the World Health Organization (WHO). In Summary, the importance of collecting medicinal plants from protected areas such as mountainous rural areas, far from mining, close to clean rivers, and regular control of values with potentially toxic elements analyzes for human health has been understood once again.

We present a fast, accurate, and robust approach for determination of free energy profiles and kinetic isotope effects for RNA 2'-O-transphosphorylation reactions with inclusion of nuclear quantum effects. We apply a deep potential range correction (DPRc) for combined quantum mechanical/molecular mechanical (QM/MM) simulations of reactions in the condensed phase. The method uses the second-order density-functional tight-binding method (DFTB2) as a fast, approximate base QM model. The DPRc model modifies the DFTB2 QM interactions and applies short-range corrections to the QM/MM interactions to reproduce ab initio DFT (PBE0/6-31G*) QM/MM energies and forces. The DPRc thus enables both QM and QM/MM interactions to be tuned to high accuracy, and the QM/MM corrections are designed to smoothly vanish at a specified cutoff boundary (6 Å in the present work). The computational speed-up afforded by the QM/MM+DPRc model enables free energy profiles to be calculated that include rigorous long-range QM/MM interactions under periodic boundary conditions and nuclear quantum effects through a path integral approach using a new interface between the AMBER and i-PI software. The approach is demonstrated through the calculation of free energy profiles of a native RNA cleavage model reaction and reactions involving thio-substitutions, which are important experimental probes of the mechanism. The DFTB2+DPRc QM/MM free energy surfaces agree very closely with the PBE0/6-31G* QM/MM results, and it is vastly superior to the DFTB2 QM/MM surfaces with and without weighted thermodynamic perturbation corrections. ¹⁸O and ³⁴S primary kinetic isotope effects are compared, and the influence of nuclear quantum effects on the free energy profiles is examined., This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Theory and Computation, copyright © 2022 American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jctc.2c00151

We develop a new deep potential-range correction (DPRc) machine learning potential for combined quantum mechanical/molecular mechanical (QM/MM) simulations of chemical reactions in the condensed phase. The new range correction enables short-ranged QM/MM interactions to be tuned for higher accuracy, and the correction smoothly vanishes within a specified cutoff. We further develop an active learning procedure for robust neural network training. We test the DPRc model and training procedure against a series of six nonenzymatic phosphoryl transfer reactions in solution that are important in mechanistic studies of RNA- cleaving enzymes. Specifically, we apply DPRc corrections to a base QM model and test its ability to reproduce free-energy profiles generated from a target QM model. We perform these comparisons using the MNDO/d and DFTB2 semiempirical models because they differ in the way they treat orbital orthogonalization and electrostatics and produce free-energy profiles which differ significantly from each other, thereby providing us a rigorous stress test for the DPRc model and training procedure. The comparisons show that accurate reproduction of the free-energy profiles requires correction of the QM/MM interactions out to 6 angstrom. We further find that the model's initial training benefits from generating data from temperature replica exchange simulations and including high-temperature configurations into the fitting procedure, so the resulting models are trained to properly avoid high-energy regions. A single DPRc model was trained to reproduce four different reactions and yielded good agreement with the free-energy profiles made from the target QM/MM simulations. The DPRc model was further demonstrated to be transferable to 2D free-energy surfaces and 1D free-energy profiles that were not explicitly considered in the training. Examination of the computational performance of the DPRc model showed that it was fairly slow when run on CPUs but was sped up almost 100-fold when using NVIDIA V100 GPUs, resulting in almost negligible overhead. The new DPRc model and training procedure provide a potentially powerful new tool for the creation of next-generation QM/MM potentials for a wide spectrum of free-energy applications ranging from drug discovery to enzyme design.

Studying the effects of UV and VUV radiation on non‐canonical DNA/RNA nucleobases allows us to compare how they release excess energy following absorption with respect to their canonical counterparts. This has attracted much research attention in recent years because of its likely influence on the origin of our genetic lexicon in prebiotic times. Here we present a CASSCF and XMS‐CASPT2 theoretical study of the photoionisation of non‐canonical pyrimidine nucleobase isocytosine in both its keto and enol tautomeric forms. We analyse their lowest energy cationic excited states including 2π+ , 2nO+ and 2nN+ and compare these to the corresponding electronic states in cytosine. Investigating lower‐energy decay pathways we find – unexpectedly ‐ that keto‐isocytosine+ presents a sizeable energy barrier potentially inhibiting decay to its cationic ground state, whereas enol‐isocytosine+ features a barrierless and consequently ultrafast pathway analogous to the one previously found for the canonical (keto) form of cytosine+. Dynamic electron correlation reduces the energy barrier in the keto form substantially (by ∼1 eV) but it is nevertheless still present. We additionally compute the UV/Vis absorption signals of the structures encountered along these decay channels to provide spectroscopic fingerprints to assist future experiments in monitoring these intricate photo‐processes., The photostability of isocytosine upon ionising radiation exposure is assessed theoretically in both keto and enol tautomeric forms. This non‐canonical base, which features analogous UV excited state reactivity to DNA nucleobase cytosine, unexpectedly displays sizeable energy barriers along the cationic excited state in its keto form that hamper the decay. Simulations suggest isocytosine is less photostable against photoionisation, a factor that might contribute to selecting the more resilient cytosine under prebiotic VUV radiation exposure.

Diketopyrrolopyrrole (DPP) is a pivotal functional group to tune the physicochemical properties of novel organic photoelectronic materials. Among multiple uses, DPP-thiophene derivatives forming a dimer through a vinyl linker were recently shown to quench the fluorescence observed in their isolated monomers. Here, we explain this fluorescence quenching using computational chemistry. The DPP-thiophene dimer has a low-lying doubly excited state that is not energetically accessible for the monomer. This state delays the fluorescence allowing internal conversion to occur first. We characterize the doubly excited state wavefunction by systematically changing the derivatives to tune the π-scaffold size and the acceptor and donor characters. The origin of this state's stabilization is related to the increase in the π-system and not to the charge-transfer features. This analysis delivers core conceptual information on the electronic properties of organic chromophores arranged symmetrically around a vinyl linker, opening new ways to control the balance between luminescence and internal conversion. ispartof: PHYSICAL CHEMISTRY CHEMICAL PHYSICS vol:24 issue:38 pages:23279-23288 ispartof: location:England status: published

The Sørensen-Mølmer gate and Milburn gate are two geometric phase gates, generating nonlinear self-interaction of a target mode via its interaction with an auxiliary mechanical mode, in the continuous- and pulsed-interaction regimes, respectively. In this paper we aim at unifying the two gates by demonstrating that the Sørensen-Mølmer gate is the continuous limit of the Milburn gate, emphasizing the geometrical interpretation in the mechanical phase space. We explicitly consider imperfect gate parameters, focusing on relative errors in time for the Sørensen-Mølmer gate and in phase angle increment for the Milburn gate. We find that, although the purities of the final states increase for the two gates upon reducing the interaction strength together with traversing the mechanical phase space multiple times, the fidelities behave differently. We point out that the difference exists because the interaction strength depends on the relative error when taking the continuous limit from the pulsed regime, thereby unifying the mathematical framework of the two gates. We demonstrate this unification in the example of an optomechanical system, where mechanical dissipation is also considered. We highlight that the unified framework facilitates our method of deriving the dynamics of the continuous-interaction regime without solving differential equations.

Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of DNA and RNA double helices is described by a homogeneous Twistable Wormlike Chain (TWLC), a semiflexible polymer model characterized by twist and bending stiffnesses. At shorter scales this model breaks down for two reasons: the elastic properties become sequence-dependent and the mechanical deformations at distal sites gets coupled. We discuss in this paper the origin of the latter effect using the framework of a non-local Twistable Wormlike Chain (nlTWLC). We show, by comparing all-atom simulations data for DNA and RNA double helices, that the non-local couplings are of very similar nature in these two molecules: couplings between distal sites are strong for tilt and twist degrees of freedom and weak for roll. We introduce and analyze a simple double-stranded polymer model which clarifies the origin of this universal distal couplings behavior. In this model, referred to as the ladder model, a nlTWLC description emerges from the coarsening of local (atomic) degrees of freedom into angular variables which describe the twist and bending of the molecule. Differently from its local counterpart, the nlTWLC is characterized by a length-scale-dependent elasticity. Our analysis predicts that nucleic acids are mechanically softer at the scale of a few base pairs and are asymptotically stiffer at longer length scales, a behavior which matches experimental data., Comment: 14 pages, 12 figures

The investigation of the behaviour of water under thermal fields is important to understand thermoelectricity of solutions, aqueous suspensions, bioelectric effects or the properties of wet materials under spatially inhomogeneous temperature conditions. Here we discuss the response of bulk water to external thermal fields using non-equilibrium molecular dynamics simulations, and five widely used forcefields: TIP4P/2005, TIP4P/2005f, OPC, SPC/E and TIP3P. These models all show the thermal polarisation (TP) effect in bulk water, namely the build-up of an electrostatic field induced by the temperature gradient. The strength of this effect is ∼0.1-1 mV K-1 at near-standard conditions for all forcefields, supporting the generality of TP. Moreover, all the models predict a temperature inversion of the polarisation field, although the inversion temperatures vary significantly across different models. We rationalise this result by deriving theoretical equations that describe the temperature inversion as a balance of the isobaric thermal expansion, dipole orientation in the thermal field and the ratio of the molecular dipole/quadrupole moments. Lower ratios lead to higher inversion temperatures. Based on our results, we conclude that the accuracy of the forcefields describing the TP effect decreases as, TIP4P/2005 ∼ TIP4P/2005f ∼ OPC > SPC/E > TIP3P. At coexistence conditions, the inversion temperature is expected to be around 400 K. Furthermore, we establish a correlation between the TP inversion temperature and the temperature corresponding to the minimum of the liquid-vapour surface potential of water.

Within Gross-Pitaevskii (GP) theory we derive the interface potential V (l) which describes the interaction between the interface separating two demixed Bose-condensed gases and an optical hard wall at a distance l. Previous work revealed that this interaction gives rise to extraordinary wetting and prewetting phenomena. Calculations that explore non-equilibrium properties by using l as a constraint provide a thorough explanation for this behavior. We find that at bulk two-phase coexistence, V (l) for both complete wetting and partial wetting is monotonic with exponential decay. Remarkably, at the first-order wetting phase transition, V(l) is independent of l. This anomaly explains the infinite continuous degeneracy of the grand potential reported earlier. As a physical application, using V(l) we study the three-phase contact line where the interface meets the wall under a contact angle theta. Employing an interface displacement model we calculate the structure of this inhomogeneity and its line tension tau. Contrary to what happens at a usual first-order wetting transition in systems with short-range forces, tau does not approach a nonzero positive constant for theta going to zero, but instead approaches zero (from below) as would be expected for a critical wetting transition. This hybrid character of tau is a consequence of the absence of a barrier in V(l) at wetting. For a typical V(l) we provide a conjecture for the exact line tension within GP theory., 18 pages, 15 figures

A range of the distinctive physical properties, comprising high surface-to-volume ratio, possibility to achieve mechanical and chemical stability after a tailored treatment, controlled quantum confinement and the room-temperature photoluminescence, combined with mass production capabilities offer porous silicon unmatched capabilities required for the development of electro-optical devices. Yet, the mechanism of the charge carrier dynamics remains poorly controlled and understood. In particular, non-radiative recombination, often the main process of the excited carrier’s decay, has not been adequately comprehended to this day. Here we show, that the recombination mechanism critically depends on the composition of surface passivation. That is, hydrogen passivated material exhibits Shockley–Read–Hall type of decay, while for oxidised surfaces, it proceeds by two orders of magnitude faster and exclusively through the Auger process. Moreover, it is possible to control the source of recombination in the same sample by applying a cyclic sequence of hydrogenation–oxidation–hydrogenation processes, and, consequently switching on-demand between Shockley–Read–Hall and Auger recombinations. Remarkably, irregardless of the recombination mechanism, the rate constant scales inversely with the average volume of individual silicon nanocrystals contained in the material. Thus, the type of the non-radiative recombination is established by the composition of the passivation, while its rate depends on the degree of the charge carriers’ quantum confinement.

Room Temperature Ionic Liquids (RTILs) attract significant interest in nanotribology. However, their microscopic lubrication mechanism is still under debate. Here, using non-equilibrium molecular dynamics simulations, we investigate the lubrication performance of ultra-thin (0.5 GPa, while bi-layers sustain pressures in the 1–2 GPa range. The compression of these films results in monolayers that can sustain loads of several GPa without significant loss in their lubrication performance. Surprisingly, in such ultra-thin films the imidazolium rings show higher orientational in-plane disorder, with and the rings adopting a tilted orientation with respect to the gold surface. The friction force and friction coefficient of the monolayers depends strongly on the structure of the gold plates, with the friction coefficient being four times higher for monolayers confined between Au(100) surfaces than for more compact Au(111) surfaces. We show that the general behaviour described here is independent of whether the metallic surfaces are modelled as polarizable or non-polarizable surfaces and speculate on the nature of this unexpected conclusion.

Activation of CO2 is the first step towards its reduction to more useful chemicals. Here we systematically investigate the CO2 activation mechanism on Cu3X (X is a first-row transition metal atom) using density functional theory computations. The CO2 adsorption energies and the activation mechanisms depend strongly on the selected dopant. The dopant electronegativity, the HOMO-LUMO gap and the overlap of the frontier molecular orbitals control the CO2 dissociation efficiency. Our calculations reveal that early transition metal-doped (Sc, Ti, V) clusters exhibit a high CO2 adsorption energy, a low activation barrier for its dissociation, and a facile regeneration of the clusters. Thus, early transition metal-doped copper clusters, particularly Cu3Sc, may be efficient catalysts for the carbon capture and utilization process. ispartof: PHYSICAL CHEMISTRY CHEMICAL PHYSICS vol:23 issue:38 pages:21738-21747 ispartof: location:England status: published

The local activation overpotential describes the electrostatic potential shift away from equilibrium at an electrode/electrolyte interface. This electrostatic potential is not entirely satisfactory for describing the reaction kinetics of a mixed ionic–electronic conducting (MIEC) solid-oxide cell (SOC) electrode where charge transfer occurs at the electrode–gas interface. Using the theory of the electrostatic potential at the MIEC–gas interface as an electrochemical driving force, charge transfer at the ceria–gas interface has been modelled based on the intrinsic dipole potential of the adsorbate. This model gives a physically meaningful reason for the enhancement in electrochemical activity of a MIEC electrode as the steam and hydrogen pressure is increased in both fuel cell and electrolysis modes. This model was validated against operando XPS data from previous literature to accurately predict the outer work function shift of thin film Sm0.2Ce0.8O1.9 in a H2/H2O atmosphere as a function of overpotential.

WO3 photoanodes offer rare stability in acidic media, but are limited by their selectivity for oxygen evolution over parasitic side reactions, when employed in photoelectrochemical (PEC) water splitting. Herein, this is remedied via the modification of nanostructured WO3 photoanodes with surface decorated PdO as an oxygen evolution co-catalyst (OEC). The photoanodes and co-catalyst particles are grown using an up-scalable aerosol assisted chemical vapour deposition (AA-CVD) route, and their physical properties characterised by X-ray diffraction (XRD), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), high-resolution transmission electron microscopy (HR-TEM) and UV-vis absorption spectroscopy. Subsequent PEC and transient photocurrent (TPC) measurements showed that the use of a PdO co-catalyst dramatically increases the faradaic efficiency (FE) of water oxidation from 52% to 92%, whilst simultaneously enhancing the photocurrent generation and charge extraction rate. The Pd oxidation state was found to be critical in achieving these notable improvements to the photoanode performance, which is primarily attributed to the higher selectivity towards oxygen evolution when PdO is used as an OEC and the formation of a favourable junction between WO3 and PdO, that drives band bending and charge separation.

Ab initio electronic excited state calculations are necessary for the quantitative study of photochemical reactions, but their accurate computation on classical computers is plagued by prohibitive resource scaling. The Variational Quantum Deflation (VQD) is an extension of the quantum-classical Variational Quantum Eigensolver (VQE) algorithm for calculating electronic excited state energies, and has the potential to address some of these scaling challenges using quantum computers. However, quantum computers available in the near term can only support a limited number of quantum circuit operations, so reducing the quantum computational cost in VQD methods is critical to their realisation. In this work, we investigate the use of adaptive quantum circuit growth (ADAPT-VQE) in excited state VQD calculations, a strategy that has been successful previously in reducing the resources required for ground state energy VQE calculations. We also invoke spin restrictions to separate the recovery of eigenstates with different spin symmetry to reduce the number of calculations and accumulation of errors in computing excited states. We created a quantum eigensolver emulation package - Quantum Eigensolver Building on Achievements of Both quantum computing and quantum chemistry (QEBAB) - for testing the proposed adaptive procedure against two existing VQD methods that use fixed-length quantum circuits: UCCGSD-VQD and k-UpCCGSD-VQD. For a lithium hydride test case we found that the spin-restricted adaptive growth variant of VQD uses the most compact circuits out of the tested methods by far, consistently recovers adequate electron correlation energy for different nuclear geometries and eigenstates while isolating the singlet and triplet manifold. This work is a further step towards developing techniques which improve the efficiency of hybrid quantum algorithms for excited state quantum chemistry, opening up the possibility of exploiting real quantum computers for electronic excited state calculations sooner than previously anticipated.

The expansion of lithium-ion batteries from consumer electronics to larger-scale transport and energy storage applications has made understanding the many mechanisms responsible for battery degradation increasingly important. The literature in this complex topic has grown considerably; this perspective aims to distil current knowledge into a succinct form, as a reference and a guide to understanding battery degradation. Unlike other reviews, this work emphasises the coupling between the different mechanisms and the different physical and chemical approaches used to trigger, identify and monitor various mechanisms, as well as the various computational models that attempt to simulate these interactions. Degradation is separated into three levels: the actual mechanisms themselves, the observable consequences at cell level called modes and the operational effects such as capacity or power fade. Five principal and thirteen secondary mechanisms were found that are generally considered to be the cause of degradation during normal operation, which all give rise to five observable modes. A flowchart illustrates the different feedback loops that couple the various forms of degradation, whilst a table is presented to highlight the experimental conditions that are most likely to trigger specific degradation mechanisms. Together, they provide a powerful guide to designing experiments or models for investigating battery degradation.

Core level photoelectron spectroscopy is a widely used technique to study amino acids. Interpretation of the individual contributions from functional groups and their local chemical environments to overall spectra requires both high-resolution reference spectra and theoretical insights, for example from density functional theory calculations. This is a particular challenge for crystalline amino acids due to the lack of experimental data and the limitation of previous calculations to gas phase molecules. Here, a state of the art multiresolution approach is used for high precision gas phase calculations and to validate core hole pseudopotentials for plane-wave calculations. This powerful combination of complementary numerical techniques provides a framework for accurate ΔSCF calculations for molecules and solids in systematic basis sets. It is used to successfully predict C and O 1s core level spectra of glycine, alanine and serine and identify chemical state contributions to experimental spectra of crystalline amino acids.

Determining stability constants of uranyl complexes with the principal functional groups in siderophores and identifying stability series is of great importance to predict which siderophore classes preferentially bind to UVI and, hence, impact uranium speciation in the environment. It also helps to develop resins for scavenging UVI from aqueous solutions. Here, we apply a recently developed computational approach to calculate log β values for a set of geochemically relevant uranium organometallic complexes using Density Functional Theory (DFT). We determined the stability series for catecholate, hydroxamate, α-hydroxycarboxylate, α-aminocarboxylate, hydroxy-phenyloxazolonate, and α-hydroxyimidazole with the uranyl cation. In this work, the stability constants (log β110) of α-hydroxyimidazolate and hydroxy-phenyloxazolonate are calculated for the first time. Our approach employed the B3LYP density functional approximation, aug-cc-pVDZ basis set for ligand atoms, MDF60 ECP for UVI, and the IEFPCM solvation model. DFT calculated log β110 were corrected using a previously established fitting equation. We find that the siderophore functional groups stability decreases in the order: α-hydroxycarboxylate bound via the α-hydroxy and carboxylate groups (log β110 = 17.08), α-hydroxyimidazolate (log β110 = 16.55), catecholate (log β110 = 16.43), hydroxamate (log β110 = 9.00), hydroxy-phenyloxazolonate (log β110 = 8.43), α-hydroxycarboxylate bound via the carboxylate group (log β110 = 7.51) and α-aminocarboxylate (log β110 = 4.73). We confirm that the stability for the binding mode of the functional groups decrease in the order: bidentate, monodentate via ligand O atoms, and monodentate via ligand N atoms. The stability series strongly suggests that α-hydroxyimidazolate is an important functional group that needs to be included when assessing uranyl mobility and removal from aqueous solutions.

Efficient photomolecular motors will be critical elements in the design and development of molecular machines. Optimisation of the quantum yield for photoisomerisation requires a detailed understanding of molecular dynamics in the excited electronic state. Here we probe the primary photophysical processes in the archetypal first generation photomolecular motor, with sub‐50 fs time resolved fluorescence spectroscopy. A bimodal relaxation is observed with a 100 fs relaxation of the Franck‐Condon state to populate a red‐shifted state with a reduced transition moment, which then undergoes multi‐exponential decay on a picosecond timescale. Oscillations due to the excitation of vibrational coherences in the S1 state are seen to survive the ultrafast structural relaxation. The picosecond relaxation reveals a strong solvent friction effect which is thus ascribed to torsion about the C−C axle. This behaviour is contrasted with second generation photomolecular motors; the principal differences are explained by the existence of a barrier on the excited state surface in the case of the first‐generation motors which is absent in the second generation. These results will help to provide a basis for designing more efficient molecular motors in the future., Generation conflict? The excited state dynamics of first‐generation molecular motors are studied by means of ultrafast time resolved fluorescence. A 100 fs structural reorganization in the excited state is followed by a slower excited state relaxation, which is influenced by solvent viscosity. The decay is accompanied by coherent vibrational excitation of modes in the excited electronic state. The observed behaviour is contrasted with that of the second‐generation motors.

The heating of a chromophore due to internal conversion and its cooling down due to energy dissipation to the solvent are crucial phenomena to characterize molecular photoprocesses. In this work, we simulated the ab initio nonadiabatic dynamics of cytosine, a prototypical chromophore undergoing ultrafast internal conversion, in three solvents-argon matrix, benzene, and water-spanning an extensive range of interactions. We implemented an analytical energy-transfer model to analyze these data and extract heating and cooling times. The model accounts for nonadiabatic effects, and excited- and ground-state energy transfer, and can analyze data from any dataset containing kinetic energy as a function of time. Cytosine heats up in the subpicosecond scale and cools down within 25, 4, and 1.3 ps in argon, benzene, and water, respectively. The time constants reveal that a significant fraction of the benzene and water heating occurs while cytosine is still electronically excited. ispartof: PHYSICAL CHEMISTRY CHEMICAL PHYSICS vol:24 issue:16 pages:9403-9410 ispartof: location:England status: published

A comparison of DFT-computed and measured infrared spectra reveals the ground state structures of a series of gas-phase silicon clusters containing a common Mn2 unit. Mn2Si12 and [Mn2Si13]+ are both axially symmetric, allowing for a clean separation of the vibrational modes into parallel (a1) and perpendicular (e1) components. Information about the Mn–Mn and Mn–Si bonding can be extracted by tracing the evolution of these modes as the cluster increases in size. In [Mn2Si13]+, where the antiprismatic core is capped on both hexagonal faces, a relatively simple spectrum emerges that reflects a pseudo-D6d geometry. In cases where the cluster is more polar, either because there is no capping atom in the lower face (Mn2Si12) or the capping atom is present but displaced off the principal axis (Mn2Si13), the spectra include additional features derived from vibrational modes that are forbidden in the parent antiprism.

Antimony sulfide (Sb2S3) and selenide (Sb2Se3) have emerged as promising earth-abundant alternatives among thin-film photovoltaic compounds. A distinguishing feature of these materials is their anisotropic crystal structures, which are composed of quasi-one-dimensional (1D) [Sb4X6]n ribbons. The interaction between ribbons has been reported to be van der Waals (vdW) in nature and Sb2X3 are thus commonly classified in the literature as 1D semiconductors. However, based on first-principles calculations, here we show that inter-ribbon interactions are present in Sb2X3 beyond the vdW regime. The origin of the anisotropic structures is related to the stereochemical activity of the Sb 5s lone pair according to electronic structure analysis. The impacts of structural anisotropy on the electronic, dielectric and optical properties relevant to solar cells are further examined, including the presence of higher dimensional Fermi surfaces for charge carrier transport. Our study provides guidelines for optimising the performance of Sb2X3-based photovoltaics via device structuring based on the underlying crystal anisotropy.

The basicity of the simplest silicone, disiloxane (H3Si−O−SiH3), is strongly affected by the Si−O−Si angle (α). We use high-level ab initio MP2/aug′-cc-pVTZ calculations and the molecular electrostatic potential (MEP) to analyze the relationship between the increase in basicity and the reduction of α. Our results clearly point out that this increase can be explained through the MEP, as the interactions between oxygen from disiloxane and the acceptors are mostly electrostatic. Furthermore, the effect of α on the tetrel bond between disiloxane and several Lewis bases can again be rationalized using the MEP. Finally, we explore the cooperativity throughout α for ternary complexes where disiloxane simultaneously interacts with a Lewis acid and a Lewis base. Both non-covalent interactions remain cooperative for all α values, although the largest cooperativity effects are not always those maximizing the binding energy in the binary complexes. Overall, the MEP remains a powerful predictor for noncovalent interactions., C. M.-F. wishes to acknowledge Dr. Malte Fugel for fruitful discussions regarding the nature of the Si−O bond and the electronic changes arising from the angular deformation of the siloxane linkage. This work was carried out with financial support from the Ministerio de Ciencia, Innovación y Universidades (Project 5931125495-125495-4-21) and Comunidad Autónoma de Madrid (PS2018/EMT-4329 AIRTEC-CM). C. M.-F. is thankful for funding from KU Leuven (PDMT2/21/041). Thanks are also given to the Centro de Computación Científica de la Universidad Autónoma de Madrid (CCC-UAM), CTI (CSIC) and VSC (Flemish Supercomputer Center) for their continued computational support.

The practical use of ionic liquids (ILs) is benefiting from a growing understanding of the underpinning structural and dynamic properties, facilitated through classical molecular dynamics (MD) simulations. The predictive and explanatory power of a classical MD simulation is inextricably linked to the underlying force field. A key aspect of the forcefield for ILs is the ability to recover charge based interactions. Our focus in this paper is on the description and recovery of charge transfer and polarisability effects, demonstrated through MD simulations of the widely used 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [C4C1im][NTf2] IL. We study the charge distributions generated by a range of ab initio methods, and present an interpolation method for determining atom-wise scaled partial charges. Two novel methods for determining the mean field (total) charge transfer from anion to cation are presented. The impact of using different charge models and different partial charge scaling (unscaled, uniformly scaled, atom-wise scaled) are compared to fully polarisable simulations. We study a range of Drude particle explicitly polarisable potentials and shed light on the performance of current approaches to counter known problems. It is demonstrated that small changes in the charge description and MD methodology can have a significant impact; biasing some properties, while leaving others unaffected within the structural and dynamic domains.

The Interfacial Thermal Conductance (ITC) is a fundamental property of materials and has particular relevance at the nanoscale. The ITC quantifies the thermal resistance between materials of different compositions or between fluids in contact with materials. Furthermore, the ITC determines the rate of cooling/heating of the materials and the temperature drop across the interface. Here, we propose a method to compute local ITCs and temperature drops of nanoparticle–fluid interfaces. Our approach resolves the ITC at the atomic level using the atomic coordinates of the nanomaterial as nodes to compute local thermal transport properties. We obtain high-resolution descriptions of the interfacial thermal transport by combining the atomistic nodal approach, computational geometry techniques, and “computational farming” using non-equilibrium molecular dynamics simulations. We use our method to investigate the ITC of nanoparticle–fluid interfaces as a function of the nanoparticle size and geometry, targeting experimentally relevant structures of gold nanoparticles: capped octagonal rods, cuboctahedrons, decahedrons, rhombic dodecahedrons, cubes, icosahedrons, truncated octahedrons, octahedrons, and spheres. We show that the ITC of these very different geometries varies significantly in different regions of the nanoparticle, increasing generally in the order face < edge < vertex. We show that the ITC of these complex geometries can be accurately described in terms of the local coordination number of the atoms in the nanoparticle surface. Nanoparticle geometries with lower surface coordination numbers feature higher ITCs, and the ITC generally increases with the decreasing particle size

Mimicking the innovative structure, design and multifunctional mechanisms of biological process based sustainable biosensor technology in living creatures is highly successful with multilingual features that draw in constantly more and more research efforts and extensive attention from the numerous species of diagnosis and clinical origins. This review will provide a comprehensive overview with respect to the innovative approach for identify, recognizing and showcasing the current advancements and key milestones accomplished in this field, aiming to provide an exclusive outlook for the bioderived materials and their most relevant applications to encourage readers to explore the uncharted realms of sustainable biointerfaces in the last 5 years.

Abstract We investigate the strong-field ion emission from the surface of isolated silica nanoparticles aerosolized from an alcoholic solution, and demonstrate the applicability of the recently reported near-field imaging at 720 nm [Rupp et al., Nat. Comm., 10(1):4655, 2019] to longer wavelength (2 $$\mu $$ μ m) and polarizations with arbitrary ellipticity. Based on the experimental observations, we discuss the validity of a previously introduced semi-classical model, which is based on near-field driven charge generation by a Monte-Carlo approach and classical propagation. We furthermore clarify the role of the solvent in the surface composition of the nanoparticles in the interaction region. We find that upon injection of the nanoparticles into the vacuum, the alcoholic solvent evaporates on millisecond time scales, and that the generated ions originate predominantly from covalent bonds with the silica surface rather than from physisorbed solvent molecules. These findings have important implications for the development of future theoretical models of the strong-field ion emission from silica nanoparticles, and the application of near-field imaging and reaction dynamics of functional groups on isolated nanoparticles. Graphical abstract