Development of an anisotropic polarizable model for the all-atom AMOEBA force field.

For planar and rigid π-conjugated molecular systems, electrostatic and inductive interactions are pivotal in governing molecular packing structures and electron polarization energies. These electrostatic interactions typically exhibit an anisotropic nature within π-conjugated systems. In this study, we utilize the atoms in molecules (AIM) theory in conjunction with linear response theory to decompose molecular polarizability into distributed atomic polarizability tensors. On the basis of atomic polarizability tensors, we extended an anisotropic polarizable model into the AMOEBA polarizable force field. Both anisotropic and isotropic polarizable models in combination with various density functional theory (DFT)-derived atomic multipoles were applied to optimize the experimental crystals of naphthalene and anthracene. Furthermore, these two types of electrostatic models, coupled with the evolutionary algorithm USPEX program, are utilized to predict the crystal structures of oligoacenes. Our findings demonstrate that the anisotropic polarizable model exhibits superior performance in crystal refinement and crystal structure prediction. This enriched anisotropic polarizable model is seamlessly integrated into the AMOEBA polarizable force field and readily applicable within our modified Tinker program.

Rapid Estimation of fwhm for OLED Emission Spectra Using Bond-Length and Bond-Order Alterations.

Color purity is crucial for achieving a high-quality organic light-emitting diode. An essential property for evaluating color purity is the full width at half-maximum (fwhm) of emission spectra. Theoretically estimating fwhm requires the detailed knowledge of vibronic coupling constants for all vibrational modes, which is time-consuming to obtain via quantum mechanical calculations, particularly for optimizing the geometry of the lowest singlet excited state. These calculations pose a bottleneck for high-throughput screening of narrowband emitters. To address this challenge, we propose a simple model to assess the reorganization energy based on the relationship between bond-length alteration (ΔBL) and vertical bond-order alteration (ΔBO) in optimized ground-state structures. Additionally, a one-mode model is employed to rapidly and effectively estimate fwhm. Our new model yields results comparable to experimental data and more accurate theoretical approaches based on vibronic coupling constants of all vibrational modes but with significantly lower computational costs. This model holds promise for the virtual screening of narrowband emitter candidates.

Transcriptomic changes and gene fusions during the progression from Barrett's esophagus to esophageal adenocarcinoma.

The incidence of esophageal adenocarcinoma (EAC) has surged by 600% in recent decades, with a dismal 5-year survival rate of just 15%. Barrett's esophagus (BE), affecting about 2% of the population, raises the risk of EAC by 40-fold. Despite this, the transcriptomic changes during the BE to EAC progression remain unclear. Our study addresses this gap through comprehensive transcriptomic profiling to identify key mRNA signatures and genomic alterations, such as gene fusions. We performed RNA-sequencing on BE and EAC tissues from 8 individuals, followed by differential gene expression, pathway and network analysis, and gene fusion prediction. We identified mRNA changes during the BE-to-EAC transition and validated our results with single-cell RNA-seq datasets. We observed upregulation of keratin family members in EAC and confirmed increased levels of keratin 14 (KRT14) using immunofluorescence. More differentiated BE marker genes are downregulated during progression to EAC, suggesting undifferentiated BE subpopulations contribute to EAC. We also identified several gene fusions absent in paired BE and normal esophagus but present in EAC. Our findings are critical for the BE-to-EAC transition and have the potential to promote early diagnosis, prevention, and improved treatment strategies for EAC.

Solvent Effect on Dative and Ionic Bond Strengths: A Unified Theory from Potential Analysis and Valence-Bond Computations.

Solvent molecules interact with a solute through various intermolecular forces. Here we employed a potential energy surface (PES) analysis to interpret the solvent-induced variations in the strengths of dative (Me3NBH3) and ionic (LiCl) bonds, which possess both ionic and covalent (neutral) characteristics. The change of a bond is driven by the gradient (force) of the solvent-solute interaction energy with respect to the focused bond length. Positive force shortens the bond length and increases the bond force constant, leading to a blue-shift of the bond stretching vibrational frequency upon solvation. Conversely, negative force elongates the bond, resulting in a reduced bond force constant and red-shift of the stretching vibrational frequency. The different responses of Me3NBH3 and LiCl to solvation are studied with valence bond (VB) theory, as Me3NBH3 and LiCl are dominated by the neutral covalent VB structure and the ionic VB structure, respectively. The dipole moment of an ionic VB structure increases along the increasing bond distance, while the dipole moment of a neutral covalent VB structure increases with the decreasing bond distance. The roles of the dominating VB structures are further examined by the geometry optimizations and frequency calculations with the block-localized wavefunction (BLW) method.

Conformational Preference of Lithium Polysulfide Clusters Li2Sx (x = 4-8) in Lithium-Sulfur Batteries.

Structures are of fundamental importance for diverse studies of lithium polysulfide clusters, which govern the performance of lithium-sulfur batteries. The ring-like geometries were regarded as the most stable structures, but their physical origin remains elusive. In this work, we systematically explored the minimal structures of Li2Sx (x = 4-8) clusters to uncover the driving force for their conformational preferences. All low-lying isomers were generated by performing global searches using the ABCluster program, and the ionic nature of the Li···S interactions was evidenced with the energy decomposition analysis based on the block-localized wave function (BLW-ED) approach and further confirmed with the quantum theory of atoms in molecule (QTAIM). By analysis of the contributions of various energy components to the relative stability with the references of the lowest-lying isomers, the controlling factor for isomer preferences was found to be the polarization interaction. Notably, although the electrostatic interaction dominates the binding energies, it contributes favorably to the relative stabilities of most isomers. The Li+···Li+ distance is identified as the key geometrical parameter that correlates with the strength of the polarization of the Sx2- fragment imposed by the Li+ cations. Further BLW-ED analyses reveal that the cooperativity of the Li+ cations primarily determines the relative strength of the polarization.

Reverse Designing the Wavelength-Specific Thermally Activation Delayed Fluorescent Molecules Using a Genetic Algorithm Coupled with Cheap QM Methods.

Genetic algorithm (GA) optimization coupled with the semiempirical intermediate neglect of differential overlap (INDO)/CIS method is presented to inversely design the red thermally activation delayed fluorescent (TADF) molecules. According to the predefined donor-acceptor (DA) library to build an ADn-type TADF candidate, we utilized the chemical notation language SMILES code to generate a TADF molecule and apply the RDKit program to produce the initial 3D molecular structure. A combined fitness function is proposed to evaluate the performance of the functional-lead TADF molecule. The fitness function includes three key parameters, i.e., the emission wavelength, the energy gap (ΔEST) between the lowest singlet (S1)- and triplet (T1)-excited states, and the oscillator strengths for electron transition from S0 and S1. A cheap QM method, i.e., INDO/CIS, on the basis of an xTB-optimized molecular geometry is applied to quickly calculate the fitness function. Finally, the GA approach is utilized to globally search for the wavelength-specific TADF molecules under our predefined DA library, and the optimum 630 nm red and 660 nm deep red TADF molecules are inversely designed according to the evolution of molecular fitness functions.

Insightful understanding of charge transfer processes in metalated phthalocyanines.

Marcus electron transfer theory coupling with quantum-mechanics (QM) calculations was applied to study the hole mobilities of a series of metalated phthalocyanine molecular crystals. The effect of metals on the frontier occupied molecular orbitals is discussed according to their eigenvalues and distributions. Temperature-dependent mobilities are rationalized by considering intermolecular interactions. Our results reveal that the central metal atoms have limited impacts on the properties of phthalocyanines. This discovery is demonstrated by their almost identical distributions and energy order of the highest occupied molecular orbitals of phthalocyanine compounds and slightly deceased internal reorganization energy and increased electron coupling compared with those of metal-free phthalocyanine. Our results reveal that the weak intermolecular interaction is mainly responsible for the notable temperature-dependent conductivity. The findings of this paper are expected to benefit the molecular design of novel phthalocyanine-based electronic devices.

Inter-anion chalcogen bonds: Are they anti-electrostatic in nature?

Inter-anion hydrogen and halogen bonds have emerged as counterintuitive linkers and inspired us to expand the range of this unconventional bonding pattern. Here, the inter-anion chalcogen bond (IAChB) was proposed and theoretically analyzed in a series of complexes formed by negatively charged bidentate chalcogen bond donors with chloride anions. The kinetic stability of IAChB was evidenced by the minima on binding energy profiles and further supported by ab initio molecular dynamic simulations. The block-localized wave function (BLW) method and its subsequent energy decomposition (BLW-ED) approach were employed to elucidate the physical origin of IAChB. While all other energy components vary monotonically as anions get together, the electrostatic interaction behaves exceptionally as it experiences a Coulombic repulsion barrier. Before reaching the barrier, the electrostatic repulsion increases with the shortening Ch⋯Cl- distance as expected from classical electrostatics. However, after passing the barrier, the electrostatic repulsion decreases with the Ch⋯Cl- distance shortening and subsequently turns into the most favorable trend among all energy terms at short ranges, representing a dominating force for the kinetic stability of inter-anions. For comparison, all energy components exhibit the same trends and vary monotonically in the conventional counterparts where donors are neutral. By comparing inter-anions and their conventional counterparts, we found that only the electrostatic energy term is affected by the extra negative charge. Remarkably, the distinctive (nonmonotonic) electrostatic energy profiles were reproduced using quantum mechanical-based atomic multipoles, suggesting that the crucial electrostatic interaction in IAChB can be rationalized within the classical electrostatic theory just like conventional non-covalent interactions.

Classical Electrostatics Remains the Driving Force for Interanion Hydrogen and Halogen Bonding.

Interanion hydrogen bonding (IAHB) and halogen bonding (IAXB) have emerged as a counterintuitive linker in a range of fascinating applications. Despite the overall repulsive (positive) binding energy, anions are trapped in a local minimum with its corresponding transition state (TS) preventing dissociation. In other words, the adduct of anions is metastable. Seemingly, the electrostatic paradigm and force field description of hydrogen/halogen bonding (HB/XB) are challenged, because of the preconceived Coulombic repulsion. Aiming at an insightful understanding of these interanion phenomena, we employed the energy decomposition approach based on the block-localized wavefunction method (BLW-ED) to investigate a series of exemplary interanion complexes. As expected, the key distinction from the conventional HB/XB lies in the electrostatic interaction, which is not increasingly repulsive as anions gradually approach to each other. Rather, there is a Coulombic barrier at a certain point. After this point, the electrostatic repulsion diminishes with the decreasing distance between anions. Differently, other energy components vary monotonically just like in conventional cases. The nonmonotonic characteristic of the electrostatic interaction in interanion complexes was reproduced using the multipole expansion in AMOEBA polarizable force field in which the state-specified atomic multipoles were adopted. This suggests that the nonmonotonicity can be well interpreted by classical electrostatic theory and there is no conceptual difference between conventional HB/XB and IAHB/IAXB. The stability of IAHB/IAXB depends on the competition between the local attractive HB/XB and the global Coulombic repulsion of net charges, though there is cooperativity between these two contrasting forces. This concise model was supported by the attractive IAHB/IAXB in modified molecular capsules, which exhibit strong quadruple HB/XBs and a considerable distance between charged substituents.

The effect of asymmetric external reorganization energy on electron and hole transport in organic semiconductors.

Understanding the relationship between charge mobilities and the molecular stacking structures of π-conjugated organic semiconducting materials is essential for their development. In this study, a quantum mechanics (QM)-derived state-specific polarizable force field (SS-PFF) is applied to explicitly estimate the external reorganization energies (λext) during electron transfer (ET) or hole transfer (HT) processes using our recently proposed two-point model (J. Phys. Chem. A, 2018, 122, 8957-8964). Different from the Marcus two-sphere model, the application of the explicit two-point model produces a notably asymmetric λext for ET and HT processes in oligoacene crystals. For the same charge transfer channels, the λext of ET is 7-10 times higher than that of HT, which results in a larger intrinsic hole mobility. This successfully rationalizes why acenes are prone to be p-type conducting materials. Perfluorination can change the polarity of the molecular surface electrostatic potential (ESP). Thus, perfluorination is a possible approach to reduce the external reorganization energies for ET reactions, which can be used to tune the order of λext of ET and HT processes. The two-point model with the SS-PFF, therefore, opens the door to revisit the intrinsic mobilities of electrons and holes in organic semiconductors.

Viral loads, lymphocyte subsets and cytokines in asymptomatic, mildly and critical symptomatic patients with SARS-CoV-2 infection: a retrospective study.

BACKGROUND: Tens of million cases of coronavirus disease-2019 (COVID-19) have occurred globally. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) attacks the respiratory system, causing pneumonia and lymphopenia in infected individuals. The aim of the present study is to investigate the laboratory characteristics of the viral load, lymphocyte subset and cytokines in asymptomatic individuals with SARS-CoV-2 infection in comparison with those in symptomatic patients with COVID-19. METHODS: From January 24, 2020, to April 11, 2020, 48 consecutive subjects were enrolled in this study. Viral loads were detected by RT-PCR from throat-swab, sputum and feces samples. Lymphocyte subset levels of CD3 + , CD4 + , and CD8 + T lymphocytes, B cells and NK cells were determined with biological microscope and flow cytometric analysis. Plasma cytokines (IL2, IL4, IL5, IL6, IL8, IL10, TNF-α, IFN-α and IFN-γ) were detected using flow cytometer. Analysis of variance (ANOVA), Chi-square or Fisher's exact test and Pearson's Correlation assay was used for all data. RESULTS: Asymptomatic (AS), mild symptoms (MS) and severe or critical cases (SCS) with COVID-19 were 11 (11/48, 22.9%), 26 (54.2%, 26/48) and 11 cases (11/48, 22.9%), respectively. The mean age of AS group (47.3 years) was lower than SCS group (63.5 years) (P < 0.05). Diabetes mellitus in AS, MS and SCS patients with COVID-19 were 0, 6 and 5 cases, respectively, and there was a significant difference between AS and SCS (P < 0.05). No statistical differences were found in the viral loads of SARS-CoV-2 between AS, MS and SCS groups on admission to hospital and during hospitalization. The concentration of CD 3 + T cells (P < 0.05), CD3 + CD4 + T cells (P < 0.05), CD3 + CD8 + T cells (P < 0.01), and B cells (P < 0.05) in SCS patients was lower than in AS and MS patients, while the level of IL-5 (P < 0.05), IL-6 (P < 0.05), IL-8 (P < 0.01) and IL-10 (P < 0.01), and TNF-α (P < 0.05) was higher. The age was negatively correlated with CD3 + T cells (P < 0.05), CD3 + CD4 + T cells (P < 0.05), and positively correlated with IL-2 (P < 0.001), IL-5 (P < 0.05), IL-6 (P < 0.05) IL-8 (P < 0.05), and IL-10 (P < 0.05). The viral loads were positively correlated with IL-2 (P < 0.001), IL-5 (P < 0.05), IL-6 (P < 0.05) IL-8 (P < 0.05) and IL-10 (P < 0.05), while negatively correlated with CD 3 + T cells (P < 0.05) and CD3 + CD4 + T cells (P < 0.05). CONCLUSIONS: The viral loads are similar between asymptomatic, mild and severe or critical patients with COVID-19. The severity of COVID-19 may be related to underlying diseases such as diabetes mellitus. Lymphocyte subset and plasma cytokine levels may be as the markers to distinguish severely degrees of disease, and asymptomatic patients may be as an important source of infection for the COVID-19.

Quantum Chemical Simulation of the Qy Absorption Spectrum of Zn Chlorin Aggregates for Artificial Photosynthesis.

Zn chlorin (Znchl) is easy to synthesize and has similar optical properties to those of bacteriochlorophyll c in the nature, which is expected to be used as a light-harvesting antenna system in artificial photosynthesis. In order to further explore the optical characteristics of Znchl, various sizes of a parallel layered Znchl-aggregate model and the THF-Znchl explicit solvent monomer model were constructed in this study, and their Qy excited state properties were simulated by using time-dependent density functional theory (TDDFT) and exciton theory. For the Znchl monomer, with a combination of the explicit solvent model and the implicit solvation model based on density (SMD), the calculated Qy excitation energy agreed very well with the experimental one. The Znchl aggregates may be simplified to a Zn36 model to reproduce the experimental Qy absorption spectrum by the Förster coupling theory. The proposed Znchl aggregate model provides a good foundation for the future exploration of other properties of Znchl and simulations of artificial light-harvesting antennas. The results also indicate that J-aggregrates along z-direction, due to intermolecular coordination bonds, are the dominant factor in extending the Qy band of Znchl into the near infrared region.

Stereoselective Synthesis of (E)-3-Alkylideneoxindoles via Gold(I)-Catalyzed Cross-Coupling of 3-Diazooxindoles with Diazoesters.

A versatile gold(I)-catalyzed cross-coupling reaction of 3-diazooxindoles with diazoesters has been presented, affording (E)-3-alkylideneoxindoles stereoselectively. Density functional theory calculations rationalized the chemo- and stereoselectivity of the reaction, which was in good agreement with experimental observations. In addition, (E)-3-alkylideneoxindoles were converted into their (Z)-isomers under UV-irradiation facilely, indicating the great advantage of this approach in stereoselective synthesis of both (E)- and (Z)-3-alkylideneoxindoles.

Resonance-assisted/impaired anion-π interaction: towards the design of novel anion receptors.

Substituents alter the electron density distribution in benzene in various ways, depending on their electron withdrawing and donating capabilities, as summarized by the empirical Hammett equation. The change of the π electron density distribution subsequently impacts the interaction of substituted benzenes or other cyclic conjugated rings with anions. Currently the design and synthesis of conjugated cyclic receptors capable of binding anions is an active field due to their applications in the sensing and removal of environmental contaminants and molecular recognition. By using the block-localized wavefunction (BLW) method, which is a variant of ab initio valence bond (VB) theory and can derive the reference resonance-free state self-consistently, we quantified the resonance-assisted (RA) or resonance-impaired (RI) phenomena in anion-π interactions from both structural and energetic perspectives. The frozen interaction, in which the electrostatic attraction is involved, has been shown to be the governing factor for the RA or RI interactions with anions. Energy analyses based on the empirical point charge (EPC) model indicated that the anion-π interactions can be simplified as the attraction between a negative point charge (anion) and a group of local dipoles, affected by the enriched or diminished π-cloud due to the resonance between the substituents and the conjugated ring. Hence, two strategies for the design of novel anion receptors can be envisioned. One is the enhancement of the magnitudes and/or numbers of local dipoles (polarized σ bonds), and the other is the reduction of π electron density in conjugated rings. For cases with the RI characteristics, "curved" aromatic molecules are preferred to be anion receptors. Indeed, extremely strong binding was found in complexes formed with fluorinated corannulene (F-CDD) and fluorinated [5]cycloparaphenylene (F-[5]CPP). Inspired by the RA phenomenon, complexes of p-, o- and m-benzoquinones with halides were revisited.

Salt-Templated Construction of Ultrathin Cobalt Doped Iron Thiophosphite Nanosheets toward Electrochemical Ammonia Synthesis.

Exploiting efficient electrocatalysts for electrochemical nitrogen reduction (NRR) is highly desired and deeply meaningful for realizing sustainable ammonia (NH3 ) production under ambient conditions. The Fe protein contains one [Fe4 S4 ] cluster and P cluster, which play an important role for transfer electron during the nitrogen fixing of nitrogenases. Based on the understanding of nitrogenase, the rising-star 2D iron thiophosphite (FePS3 ) nanomaterials may be highly active electrocatalysts toward NRR due to the ideal elemental composition. In this work, 2D FePS3 nanosheets are successfully synthesized by a facile salt-templated method. The FePS3 nanosheets show better electrocatalytic NH3 yield and faradaic efficiency (FE) than Fe2 S3 , which demonstrates that the P element indeed improves the NRR activity of Fe-S. Theoretically, Co incorporation not only effectively prompts the conductivity of FePS3 , but also enhances the catalytic activities of Fe-edge sites. Experimentally, Co-doped FePS3 (Co-FePS3 ) nanosheets exhibit a remarkable electrocatalytic performance toward NRR, such as high NH3 yield rate of 90.6 µg h-1 mgcat-1 , high FE of 3.38%, and an excellent long-term stability. Being the first theoretical and experimental report regarding FePS3 -based electrocatalyst toward NRR, this work represents an important beginning to the family of metal thiophosphite as advanced electrocatalysts toward NRR.

Theoretical Understanding of Electrocatalytic Hydrogen Production Performance by Low-Dimensional Metal-Organic Frameworks on the Basis of Resonant Charge-Transfer Mechanisms.

The exploration of low-cost and efficient electrocatalysts for the hydrogen evolution reaction (HER) is a prerequisite for large-scale hydrogen fuel generation. The understanding of the electronic properties of electrocatalysts plays a key role in this exploration process. In this study, our first-principles results demonstrate that the catalytic performance of the 1D metal-organic frameworks (MOFs) can be significantly influenced by engineering the composite of the metal node. Using the Gibbs free energy of the adsorption of hydrogen atoms as a key descriptor, we found that Ni- and Cr-based dithiolene MOFs possess better hydrogen evolution performance, and the much different efficiencies can be ascribed to their electronic resonance structures [TM3+(L2-)(L2-)]- ↔ [TM2+(L•-)(L2-)]-. The [TM2+(L•-)(L2-)]- structure is preferred due to the higher activity of the catalytic site L with more radical features, and the stabilized [TM2+(L•-)(L2-)]- structure of the Cr- and Ni-based MOFs can be ascribed to the electronic configurations of their TM2+ cations with half-occupied and fully occupied valence orbitals. Our results therefore reveal a novel strategy for optimizing the electronic structures of materials on the basis of the resonant charge-transfer mechanism for their practical applications.

State-specific electrostatic potential descriptors for estimating solvatochromic effects.

The Lippert-Mataga equation is used widely to describe the solvatochromic effects of fluorescent molecules through the evaluation of solute-solvent interactions on the basis of the point-dipole model. A large dipole deviation of molecules in the ground-state and the lowest excited-state is a basic requirement for the design of a polarity-sensitive fluorescent probe. Some recently synthesized probes with center-symmetry have near zero dipole deviation while undergoing notably solvatochromic behaviors. Thus, it is necessary to find a new method beyond the Lippert-Mataga model to qualitatively estimate the molecular solvent shifts. To this end, a state-specific descriptor (SSD) based on molecular surface electrostatic potentials (ESP) is proposed to explain the solvatochromic behaviors of the well-studied coumarin C153 and center-symmetric DCB-1d. In contrast to the experimental solvent shifts and state-specific TD-DFT calculations, the SSD successfully explains the solvatochromic effect of C153 and DCB-1d molecules. In addition, the SSD was tested by using eight selected polarity-sensitive fluorescent molecules. The SSD was found to provide a good linear relationship with solvatochromism.

First-Principles Determination of Active Sites of Ni Metal-Based Electrocatalysts for Hydrogen Evolution Reaction.

The determination of active sites of materials is essential for the molecular design of high-performance catalysts. In this study, the first-principles method is applied to investigate the active sites of low-cost Ni metal-based electrocatalysts for hydrogen evolution reactions (HER), which is a promising alternative to expensive Pt metal-based catalysts. The adsorption of hydrogen on different sites of pristine and partially oxidized Ni(111) surface is investigated. All of the possible configurations have been systematically investigated here with the consideration of their Boltzmann distribution. Using the Gibbs free energy of intermediate H atoms (Δ GH*) as a descriptor, it is found that the Δ GH* increases with the increase of the coverage of oxygen atoms. The slightly oxidized surface Ni atoms are theoretically identified to be the best catalytic centers for the electrocatalytic HERs when the coverage of oxygen is considerably low. On the basis of the analyses of Bader charge distribution and density of states, our results reveal that the superior performance of the slightly oxidized surface Ni atoms can be ascribed to the optimal electronic properties.

Explicit Method To Evaluate the External Reorganization Energy of Charge-Transfer Reactions in Oligoacene Crystals Using the State-Specific Polarizable Force Field.

The state-specific polarizable force field (SS-PFF) are parametrized for neutral and cationic oligoacenes based on QM calculations. The SS-PFF is applied to explicitly evaluate the electron-phonon interaction for localized hole-carrier charge transfer (CT) reactions in oligoacene crystals. A two-point model is proposed to estimate the total reorganization energy including internal and external contributions for hole-carrier CT reactions in oligoacene crystals. Orientation and separation dependent external reorganization energy are well described according to the potential energy surface of SS-PFF. Moreover, increasing the temperature leads to a small increase of the external reorganization energy of CT reactions.