JANPA: An open source cross-platform implementation of the Natural Population Analysis on the Java platform

Metalloid-Organic Intermolecular Complexes with Charge State-Controlled Conformations

Shape alterations of molecular systems, induced by their (electric) charging/discharging, could facilitate useful electronic and/or mechanical functions in molecular-scale devices and machines. The present study reports structures, stabilities, charge distributions, and IR spectra for a group of complexes of a main-group metalloid (boron) atom with hydrocarbon molecules. The considered systems include the smallest species demonstrating the basic principle of operation, as well as their size-extended analogues, generalizing it to larger counterparts based on such units. The system geometries vary considerably between neutral and ionic counterparts and exhibit two-three typical conformations related to twisting by up to about 90 degrees. The predicted structures correlate with specific infrared spectra, which can enable their experimental identification and transformation tracking. The above-mentioned characteristics suggest the potential utility of such systems for intermolecular switches, with the possible spectral monitoring of their functioning.

Theoretical Evaluation of Fluorinated Resazurin Derivatives for In Vivo Applications

Primarily owing to the pronounced fluorescence exhibited by its reduced form, resazurin (also known as alamarBlue®) is widely employed as a redox sensor to assess cell viability in in vitrostudies. In an effort to broaden its applicability for in vivo studies, molecular adjustments are necessary to align optical properties with the near-infrared imaging window while preserving redox properties. This study delves into the theoretical characterisation of a set of fluorinated resazurin derivatives proposed by Kachur et al., 2015 examining the influence of fluorination on structural and electrochemical properties. Assuming that the conductor-like polarisable continuum model mimics the solvent effect, the density functional level of theory combining M06-2X/6-311G* was used to calculate the redox potentials. Furthermore, (TD-)DFT calculations were performed with PBE0/def2-TZVP to evaluate nucleophilic characteristics, transition states for fluorination, relative energies, and fluorescence spectra. With the aim of exploring the potential of resazurin fluorinated derivatives as redox sensors tailored for in vivo applications, acid-base properties and partition coefficients were calculated. The theoretical characterisation has demonstrated its potential for designing novel molecules based on fundamental principles.

Insights into the Effect of Charges on Hydrogen Bonds

Previous computational and experimental studies showed that charges located at the surroundings of hydrogen bonds can exert two opposite effects on them: rupture or strengthening of the hydrogen bond. This work aims to generalize the effect of charges in different hydrogen-bonded systems and to propose a coherent explanation of this effect. For these purposes, 19 systems with intra- and intermolecular hydrogen bonds were studied computationally with DFT. The FT-IR spectra of the systems were simulated, and two energy components of the hydrogen bond were studied separately to determine their variation upon the presence of a charge: charge transfer and molecular overlap. It was determined that either the breaking or strengthening of the hydrogen bond can be favored one over the other, for instance, depending on the heteroatom involved in the hydrogen bond. In addition, it is showed that the strengthening of the hydrogen bond by the presence of a charge is directly related to the decrease in charge transfer between the monomers, which is explained by an increase in molecular overlapping, suggesting a more covalent character of the interaction. The understanding of how hydrogen bonds are affected by charges is important, as it is a key towards a strategy to manipulate hydrogen bonds at convenience.

Ru(II) Complexes with Protic- and Anionic-Naked-NHC Ligands for Cooperative Activation of Small Molecules

A set of ruthenium(II)-protic-N-heterocyclic carbene complexes, [Ru(NNCH )(PPh3 )2 (X)]Cl (1, X=Cl and 2, X=H) and their deprotonated forms [Ru(NNC)(PPh3 )2 (X)] (1', X=Cl and 2', X=H), in which NNC is a new unsymmetrical pincer ligand, are reported. The four complexes are interconvertible by simple acid-base chemistry. The combined theoretical and spectroscopic investigations indicate charge segregation in anionic-NHC complexes (1' and 2') and can be described from a Lewis pair perspective. The chemical reactivity of deprotonated complex 1' shows cooperative small molecule activation. Complex 1' activates H-H bond of hydrogen, C(sp3 )-I bond of iodomethane, and C(sp)-H bond of phenylacetylene. The activation of CO2 using anionic NHC complex 1' at moderate temperature and ambient pressure and subsequent conversion to formate is also described. All the new compounds have been characterized using ESI-MS, 1 H, 13 C, and 31 P NMR spectroscopy. Molecular structures of 1, 2, and 2' have also been determined with single-crystal X-ray diffraction. The cooperative small molecule activation perspective broadens the scope of potential applications of anionic-NHC complexes in small molecule activation, including the conversion of carbon dioxide to formate, a much sought after reaction in the renewable energy and sustainable development domains.

Sport training damage prevention based on hybrid image retrieval scheme

The web service is made of a variety of complex systems, but the core part is still a web service. This service maximizes the user's demand user satisfaction, the web service can be recommended according to the user's needs, the current Web service technology Not very mature, there is also an improved point in research we extracted a model, this model is the model of Hash, in which we can join the hash layer behind the full chain, by reducing the hash layer The number of nodes is low-level feature and compared with the current programs, we propose advice to network parameters in the model, because this can be used in model training, this algorithm can be left Setting the rate of learning and speeds up the speed of the model training. This model can play a very important role in the campus life, but if this model is applied to the competitive critical project, it may generate a motion damage, which occurs in this motion damage. The reason is because the intensity of the project is high, the rhythm is fast and strong, so in order to understand the damage status and damage characteristics of college students in the exercise process, we have conducted risk factors, and some precautions we can Do our best to reduce the phenomenon of sports injuries in college athletes, which is important for students' movement development.

Quantum Descriptors for Predicting and Understanding the Structure-Activity Relationships of Michael Acceptor Warheads

Predictive modeling and understanding of chemical warhead reactivities have the potential to accelerate targeted covalent drug discovery. Recently, the carbanion formation free energies as well as other ground-state electronic properties from density functional theory (DFT) calculations have been proposed as predictors of glutathione reactivities of Michael acceptors; however, no clear consensus exists. By profiling the thiol-Michael reactions of a diverse set of singly- and doubly-activated olefins, including several model warheads related to afatinib, here we reexamined the question of whether low-cost electronic properties can be used as predictors of reaction barriers. The electronic properties related to the carbanion intermediate were found to be strong predictors, e.g., the change in the Cβ charge accompanying carbanion formation. The least expensive reactant-only properties, the electrophilicity index, and the Cβ charge also show strong rank correlations, suggesting their utility as quantum descriptors. A second objective of the work is to clarify the effect of the β-dimethylaminomethyl (DMAM) substitution, which is incorporated in the warheads of several FDA-approved covalent drugs. Our data suggest that the β-DMAM substitution is cationic at neutral pH in solution and promotes acrylamide's intrinsic reactivity by enhancing the charge accumulation at Cα upon carbanion formation. In contrast, the inductive effect of the β-trimethylaminomethyl substitution is diminished due to steric hindrance. Together, these results reconcile the current views of the intrinsic reactivities of acrylamides and contribute to large-scale predictive modeling and an understanding of the structure-activity relationships of Michael acceptors for rational TCI design.

Main-Group Metal Complexes of Benzene: Predicted Features of Stabilization and Isomerization

Complexes of metal atoms with organic molecules represent a broad variety of systems with many important applications, e.g., in metal-organic interfaces and organometallic chemistry. One class involves aromatic species like benzene (Bz). Here, such complexes with second-group metals are investigated systematically in terms of structure and shape, stability and isomerization, charge distribution and aromaticity, and polarity and IR spectra. Three groups of isomers are identified, varying from metastable to stable ones, in effect featuring "physisorption" or "chemisorption". In particular, the high polarity of binary complexes and nonadditive stabilization of ternary systems for some isomers are found. Also, the Bz component's shape alteration for different isomers and system sizes and related aromaticity variations are predicted to be considerable. Property evolution for the series of metal components is analyzed.

A novel heteroleptic Cu(II)-phenanthroline-UDCA complex as lipoxygenase inhibitor and ER-stress inducer in cancer cell lines

A new heteroleptic copper(II) compound named C0-UDCA was prepared by reaction of [Cu(phen)₂(OH₂)](ClO₄)₂ (C0) with the bile ursodeoxycholic acid (UDCA). The resulting compound is able to inhibit the lipoxygenase enzyme showing more efficacy than the precursors C0 and UDCA. Molecular docking simulations clarified the interactions with the enzyme as due to allosteric modulation. The new complex shows antitumoral effect on ovarian (SKOV-3) and pancreatic (PANC-1) cancer cells at the Endoplasmic Reticulum (ER) level by activating the Unfolded Protein Response. In particular, the chaperone BiP, the pro-apoptotic protein CHOP and the transcription factor ATF6 are upregulated in the presence of C0-UDCA. The combination of Intact Cell MALDI-MS and statistical analysis have allowed us to discriminate between untreated and treated cells based on their mass spectrometry fingerprints.

Intermolecular Interactions in G Protein-Coupled Receptor Allosteric Sites at the Membrane Interface from Molecular Dynamics Simulations and Quantum Chemical Calculations

Allosteric modulators are called promising candidates in G protein-coupled receptor (GPCR) drug development by displaying subtype selectivity and more specific receptor modulation. Among the allosteric sites known to date, cavities at the receptor-lipid interface represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability, the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze interactions in the allosteric sites of the PAR2, C5aR1, and GCGR receptors in three lipid compositions using molecular dynamics simulations. In addition, we performed quantum chemical calculations involving the symmetry-adapted perturbation theory (SAPT) and the natural population analysis to quantify the strength of intermolecular interactions. We show that besides classical hydrogen bonds, weak polar interactions such as O-HC, O-Br, and long-range electrostatics with the backbone amides contribute to the stability of allosteric modulators at the receptor-lipid interface. The allosteric cavities are detectable in various membrane compositions. The availability of polar atoms for interactions in such cavities can be assessed by water molecules from simulations. Although ligand-lipid interactions are weak, lipid tails play a role in ligand binding pose stability and the size of allosteric cavities. We discuss physicochemical aspects of ligand binding at the receptor-lipid interface and suggest a compound library enriched by weak donor groups for ligand search in such sites.

The role of the intermediate triplet state in iron-catalyzed multi-state C-H activation

Efficient activation and functionalization of the C-H bond under mild conditions are of a great interest in chemical synthesis. We investigate the previously proposed spin-accelerated activation of the C(sp²)-H bond by a Fe(II)-based catalyst to clarify the role of the intermediate triplet state in the reaction mechanism. High-level electronic structure calculations on a small model of a catalytic system utilizing the coupled cluster with the single, double, and perturbative triple excitations [CCSD(T)] are used to select the density functional for the full-size model. Our analysis indicates that the previously proposed two-state quintet-singlet reaction pathway is unlikely to be efficient due to a very weak spin-orbit coupling between these two spin states. We propose a more favorable multi-state quintet-triplet-singlet reaction pathway and discuss the importance of the intermediate triplet state. This triplet state facilitates a spin-accelerated reaction mechanism by strongly coupling to both quintet and singlet states. Our calculations show that the C-H bond activation through the proposed quintet-triplet-singlet reaction pathway is more thermodynamically favorable than the single-state quintet and two-state singlet-quintet mechanisms.

Kernel charge equilibration: efficient and accurate prediction of molecular dipole moments with a machine-learning enhanced electron density model

State-of-the-art machine learning (ML) interatomic potentials use local representations of atomic environments to ensure linear scaling and size-extensivity. This implies a neglect of long-range interactions, most prominently related to electrostatics. To overcome this limitation, we herein present a ML framework for predicting charge distributions and their interactions termed kernel charge equilibration (kQEq). This model is based on classical charge equilibration (QEq) models expanded with an environment-dependent electronegativity. In contrast to previously reported neural network models with a similar concept, kQEq takes advantage of the linearity of both QEq and Kernel Ridge Regression to obtain a closed-form linear algebra expression for training the models. Furthermore, we avoid the ambiguity of charge partitioning schemes by using dipole moments as reference data. As a first application, we show that kQEq can be used to generate accurate and highly data-efficient models for molecular dipole moments.

Surface-Enhanced Raman Spectroscopy Substrates: Plasmonic Metals to Graphene

Surface-enhanced Raman spectroscopy (SERS), a marvel that uses surfaces to enhance conventional Raman signals, is proposed for a myriad of applications, such as diagnosis of diseases, pollutants, and many more. The substrates determine the SERS enhancement, and plasmonic metallic nanoparticles such as Au, Ag, and Cu have dominated the field. However, the last decades have failed to translate SERS prototypes into real-life applications. Irreproducibility on the SERS signal that stems from the roughened SERS substrates is the main causative factor for this observation. To mitigate irreproducibility several two-dimensional (2-D) substrates have been sought for use as possible alternatives. Application of 2-D graphene substrates in Raman renders graphene-enhanced Raman spectroscopy (GERS). This account used density functional theory (DFT) substantiated with experimental Raman to compare the enhancement capabilities of plasmonic Au nanoparticles (SERS), graphene substrate (GERS), and coupling of the two SERS and GERS substrates. The DFT also enabled the study of the SERS and GERS systems molecular orbital to gain insight into their mechanisms. The amalgamation of the SERS and GERS occurrence, i.e., graphene doped with plasmonic metallic substrates showed a pronounced enhancement and matched the Au-driven enhancement emanating from both electromagnetic and charge transfer SERS and GERS mechanisms.

Computational investigation of enhanced properties in functionalized carbon nanotube doped polyvinyl alcohol gel electrolyte systems

Recently, functionalized carbon nanotubes (fCNTs) were shown to increase the mechanical strength, thermal stability, and ionic conductivity in polyvinyl alcohol (PVA) based gel electrolytes (GE) for Zn ion batteries. However, questions remain about the origin of the property enhancement and the interactions between components of GEs. In this work, we employ density functional theory calculations to analyze the interactions between fCNT, PVA, and Zn ions. CNTs with increasing numbers of carboxyl (-COOH) functional groups and PVA chains with varying lengths were studied. We found that increasing the number of -COOH on the CNTs enhanced the adsorption energies (E_ads) of PVA, and E_ads also increased as the number of monomers increased. We then modelled the coordination of a Zn ion in fCNT-PVA complexes. Our results suggest that strong fCNT-PVA interactions contribute to the enhanced mechanical strength, while the enhanced ionic conductivity is partly owing to weak Zn adsorption.

The first copper(ii) complex with 1,10-phenanthroline and salubrinal with interesting biochemical properties

The novel copper complex [Cu(phen)2(salubrinal)](ClO4)2 (C0SAL) has been synthesised and characterised. Copper(ii) is coordinated by salubrinal through the thionic group, as shown by the UV-Vis, IR, ESI-MS and tandem mass results, together with the theoretical calculations. The formed complex showed a DPPH radical scavenging ability higher than that of salubrinal alone. Studies on lipid oxidation inhibition showed that the C0SAL concentration, required to inhibit the enzyme, was lower than that of salubrinal. The inhibition of the enzyme could take place via allosteric modulation, as suggested by docking calculations. C0SAL showed a good cytotoxic activity on A2780 cells, 82 fold higher than that of the precursor salubrinal and 1.4 fold higher than that of [Cu(phen)2(H2O)](ClO4)2. Treatment with C0SAL in SKOV3 ovarian cancer cells induced expression of GRP-78 and DDIT3 regulators of ER-stress response. The cytotoxic effect of C0SAL was reverted in the presence of TUDCA, suggesting that C0SAL induces cell death through ER-stress. In A2780 cells treated with C0SAL γ-H2AX was accumulated, suggesting that DNA damage was also involved.

Electronic States of CoSin-/0/+ (n = 1-3) Clusters from Density Matrix Renormalization Group-CASPT2 Calculations

Density matrix renormalization group-CASPT2 (DMRG-CASPT2), CASPT2, and density functional theory are employed to describe the complicated geometrical and electronic structures of CoSi_n^-/0/+ (n = 1-3) clusters. The active spaces of DMRG-CASPT2 are extended to 23 orbitals. The DMRG-CASPT2 method with such large active spaces is reasonable to provide highly accurate relative energies of the electronic states. The pure BP86, PBE, and TPSS functionals appear to be suitable to compute the relative energies of the electronic states of cobalt-doped silicon clusters. The leading configurations, bond distances, vibrational frequencies, normal modes, and relative energies of the electronic states are reported. The electron detachment energies of the removals of one electron from the anionic and neutral clusters are estimated. All six bands in the photoelectron spectrum of CoSi₃^- are interpreted based on the computed electron detachment energies and Franck-Condon factor simulations.

Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase

Human manganese superoxide dismutase is a critical oxidoreductase found in the mitochondrial matrix. Concerted proton and electron transfers are used by the enzyme to rid the mitochondria of O₂^•−. The mechanisms of concerted transfer enzymes are typically unknown due to the difficulties in detecting the protonation states of specific residues and solvent molecules at particular redox states. Here, neutron diffraction of two redox-controlled manganese superoxide dismutase crystals reveal the all-atom structures of Mn³⁺ and Mn²⁺ enzyme forms. The structures deliver direct data on protonation changes between oxidation states of the metal. Observations include glutamine deprotonation, the involvement of tyrosine and histidine with altered pK_as, and four unusual strong-short hydrogen bonds, including a low barrier hydrogen bond. We report a concerted proton and electron transfer mechanism for human manganese superoxide dismutase from the direct visualization of active site protons in Mn³⁺ and Mn²⁺ redox states.

Human manganese superoxide dismutase (MnSOD) is an oxidoreductase that uses concerted proton and electron transfers to reduce the levels of superoxide radicals in mitochondria, but mechanistic insights into this process are limited. Here, the authors report neutron crystal structures of Mn³⁺SOD and Mn²⁺SOD, revealing changes in the protonation states of key residues in the enzyme active site during the redox cycle.

Expanding the Family of Octahedral Chiral-at-Metal Cobalt(III) Catalysts by Introducing Tertiary Amine Moiety into the Ligand

Chiral metal-templated complexes are attractive catalysts for organic synthetic transformations. Herein, we introduce a novel chiral cobalt(III)-templated complex based on chiral trans-3,4-diamino-1-benzylpyrrolidine and 3,5-di-tert-butyl-salicylaldehyde which features both hydrogen bond donor and Brønsted base functionalities. The obtained complexes were fully characterized by 1H, 13C NMR, IR-, UV-vis, CD-spectroscopy and by a single X-ray diffraction analysis. It was shown that chlorine anion is connected with amino groups of the complex via a hydrogen bonding. DFT calculations of charges and molecular electrostatic potential of the cobalt(III) complex showed that the basicity of the complex is certainly diminished as compared with the routine tertiary amines but the acidity of the conjugated acid of the complex should be increased. Thus, the catalytic potential of the complex may be much greater as a chiral acid than a chiral base. We believe that this work opens a new way in chiral bifunctional catalyst design.

Hydroxylated 3-(pyridin-2-yl)coumarins as radical scavengers with potent lipoxygenase inhibitor activity

Hydroxylated 3-(pyridin-2-yl)coumarins show radical scavenging activity and are able to inhibit soybean lipoxygenase.

Magnetic ion-exchange (MIEX) resin for perfluorinated alkylsubstance (PFAS) removal in groundwater: Roles of atomic charges for adsorption

In this study, magnetic ion exchange (MIEX) resin was evaluated to remove six carboxylic and three sulfonic PFAS at environmentally relevant concentrations (∼300 ng/L) in groundwater with low organic content and aromaticity (0.78 mg/L of dissolved organic carbon, DOC and 0.96 L mg^-1m^-1 of specific UV absorbance, SUVA). In order to evaluate PFAS adsorption, the apparent equilibrium constant for PFAS adsorption in a dilute system was derived as an indicator of the adsorption capacity of MIEX. In adsorption of PFAS, hydrophobic interactions induced by difluoromethylene and trifluoromethyl groups are known to be effective. However, the hydrophobic and charge interactions caused by such functional groups are not easily differentiable from each other since both are additive with respect to the chain length. In this study, the total negative atomic charge [∑Q_i(-)] was calculated using density functional theory (DFT) calculation and correlated with the apparent equilibrium constants. The negative atomic charge showed better correlation than the hydrophobicity (log D_ow at pH 7) of PFAS, suggesting that the charge interaction would be a more plausible role of fluorinated moieties for adsorption in the MIEX process than the hydrophobic interaction. This was also bolstered by the similar adsorption kinetics and equilibrium of PFOS (log D_ow = 3.05) and its less hydrophobic isomer (log D_ow = 2.79), but with almost identical total negative atomic charge (8.05 and 8.06 of ∑Q_i(-), respectively). The regeneration efficiency of MIEX was also assessed. Almost complete restoration of PFAS adsorption capacity was achieved after 30 min of a regeneration process with a 10% w/w NaCl solution as a regenerant. The efficient regeneration was attributed to the effective desorption of dissolved organic matter that occupied sorptive sites predominantly.

A search of a quantitative quantum-chemical approach for radiolytic stability prediction

Radiolytic stability is one of the main requirements of the substances that are used in the chemistry of nuclear cycle or in the radiopharmaceutical chemistry. Herein, we proposed an approach for the prediction of radiolytic stability by the estimation of the molecular reactivity. The DFT calculations of the atom-wise reactivity descriptor were made for a number of organic molecules. The theoretical simulations were validated by the experimental data. We irradiated the molecules by gamma-radiation and studied the products of radiolysis and changes in the molecular concentration by HPLC-MS analysis. The importance of the inclusion of the conformational influence and the steric accessibility in the calculation is shown in this study. We presente a new chemical reactivity descriptor (CRD) and recommend using CRD as the new quantitative estimation of the reactivity. A good correlation between the CRD and the constants of the radiolysis was obtained.

NWChem: Past, present, and future

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

Psi4 1.4: Open-source software for high-throughput quantum chemistry

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.

Geometric and Electronic Structures of VB40/+ Clusters and Reactivity of the Cationic Cluster with Methane from Quantum Chemical Calculations

Quantum chemical methods have been employed to study the geometric and electronic structures of VB₄^0/+ clusters and the mechanism of the reaction of the cationic clusters with methane. It was found that the ground states of the neutral and cationic clusters were ⁴A' and ³A' of a planar isomer in C_s symmetry in which vanadium atom side-on binds to the rhombic B₄ moiety. The ionization energy of the neutral cluster was calculated to be 7.13 eV at the CCSD(T) level. The reaction pathways on the triplet and quintet potential energy profiles of the dehydrogenation and elimination of V⁺ in the reaction of VB₄⁺ cluster with methane were established based on the BPW91 functional calculations. Both of the dehydrogenation and elimination of V⁺ in the reaction of VB₄⁺ cluster with methane were initiated by the B₄ moiety of the VB₄⁺ cluster, and these two reaction channels were thermodynamically and kinetically favorable. The dehydrogenation and elimination of V⁺ in the reaction of VB₄⁺ cluster with methane were exothermic processes.