Independent gradient model based on Hirshfeld partition: A new method for visual study of interactions in chemical systems.

The powerful independent gradient model (IGM) method has been increasingly popular in visual analysis of intramolecular and intermolecular interactions in recent years. However, we frequently observed that there is an evident shortcoming of IGM map in graphically studying weak interactions, that is its isosurfaces are usually too bulgy; in these cases, not only the graphical effect is poor, but also the color on some areas on the isosurfaces is inappropriate and may lead to erroneous analysis conclusions. In addition, the IGM method was originally proposed based on promolecular density, which is quite crude and does not take actual electronic structure into account. In this article, we propose an improvement version of IGM, namely IGM based on Hirshfeld partition of molecular density (IGMH), which replaces the free-state atomic densities involved in the IGM method with the atomic densities derived by Hirshfeld partition of actual molecular electron density. This change makes IGM have more rigorous physical background. A large number of application examples in this article, including molecular and periodic systems, weak and chemical bond interactions, fully demonstrate the important value of IGMH in intuitively understanding interactions in chemical systems. Comparisons also showed that the IGMH usually has markedly better graphical effect than IGM and overcomes known problems in IGM. Currently IGMH analysis has been supported in our wavefunction analysis code Multiwfn (http://sobereva.com/multiwfn). We hope that IGMH will become a new useful method among chemists for exploring interactions in wide variety of chemical systems.

Efficient detection for Nitrofurazone based on novel Ag2S QDs/g-C3N4 fluorescent probe.

In the paper, a novel fluorescent probe based on Ag2S QDs/g-C3N4 composite was synthesized by loading Ag2S quantum dots (Ag2S QDs) on the surface of g-C3N4 through in-situ synthesis method and developed to detect Nitrofurazone (NFZ) sensitively. The results showed that the linear detection range of Ag2S QDs/g-C3N4 to NFZ was 0-30 µM, with a low detection limit of 0.054 µM. The results of time-fluorescence-resolved spectroscopy and UV-vis absorption spectroscopy exhibited that the possible detection mechanism of Ag2S QDs/g-C3N4 to NFZ was proposed to be Internal Filtration Effect (IFE). Moreover, Multiwfn wavefunction analysis was employed to uncover the possible interaction between the Ag2S QDs/g-C3N4 and NFZ, thereby further revealing the fluorescence detection mechanism from the scale of atoms. Combining experiments and theoretical calculations, we proposed the sensing mechanism of the formation of non-fluorescent ground state complex linked by hydrogen bonds. This work indicated that the Ag2S QDs/g-C3N4 composite processed the ability to detect NFZ efficiently and sensitively.

Facile immobilization of ethylenediamine tetramethylene-phosphonic acid into UiO-66 for toxic divalent heavy metal ions removal: An experimental and theoretical exploration.

By the facile immobilization of ethylenediamine tetramethylene-phosphonic acid (EDTMPA) onto the surface and into the defects of UiO-66, a stable and efficient adsorbent named UiO-66-EDTMPA was obtained for the first time. In terms of removing aqueous heavy metal ions (Pb2+, Cd2+, Cu2+), the maximum adsorption capacities of UiO-66-EDTMPA reached 558.67, 271.34 and 210.89 mg/g, which were 8.77 (Pb2+), 5.63 (Cd2+) and 5.19 (Cu2+) times higher than raw UiO-66 respectively. The adsorption behavior of three heavy metal ions on UiO-66 and UiO-66-EDTMPA were investigated and compared through batch control experiments and theoretical studies. The main factors on adsorption progress (i.e., the dosage of EDTMPA, pH, ionic strength, co-existing ions, initial concentration, contact time, temperature) were explored, and the critical characterization (i.e., SEM, TEM, XRD, FT-IR, TG-DTG, XPS, N2 adsorption-desorption test) were performed. Molecular dynamics (MD) simulation (radial distribution functions (RDF) and mean square displacement (MSD)) were also applied to reveal the adsorption behavior. Besides, two new quantum chemical analyses (Hirshfeld surface and independent gradient model (IGM)) were introduced into the interaction analysis between UiO-66 and EDTMPA. The complete results showed that (1) where the hydrogen bond and (vdW) connect EDTMPA to UiO-66. (2) The coordination between O, N atoms of EDTMPA and heavy metal ions (Pb2+, Cd2+, Cu2+) resulted in spontaneous adsorption. (3) The adsorption behavior agreed with Langmuir and pseudo-second-order model, endothermic reaction. In addition, the desorption and reusability study showed promising stable and sustainable performance. This work has some guiding significance for the experimental and theoretical study of removing heavy metal ions from aqueous solutions by MOF or modified MOF materials.

Simple, reliable, and universal metrics of molecular planarity.

Planarity is a very important structural character of molecules, which is closely related to many molecular properties. Unfortunately, there is currently no simple, universal, and robust way to measure molecular planarity. In order to fill this evident gap, we propose two metrics of molecular planarity, namely molecular planarity parameter (MPP) and span of deviation from plane (SDP), to quantitatively characterize planarity of molecules. MPP reflects the overall degree of deviation of the structure from a plane, while SDP represents the span of the structural deviation relative to the fitting plane; respectively, they are complementary to each other. The examples in this article demonstrate that these metrics have strong rationality and practicality. They can not only be used to investigate the planarity of the entire molecule, but also measure the planarity of local structures, and they can even be employed to study variation of molecular planarity during a dynamic process. In addition, we also propose a new representation, namely coloring atoms according to their signed deviation distance to the fitting plane. This kind of map allows researchers to intuitively and quickly recognize position of the atoms in the system relative to the fitting plane. It can be seen from the examples that this representation is very useful in graphically exhibiting molecular planarity. The methods proposed in this work have been implemented in our open-source analysis code Multiwfn, which can be freely obtained via http://sobereva.com/multiwfn . The use is very simple and rich file formats are supported as input file.

Adsorption of two ß-blocker pollutants on modified montmorillonite with environment-friendly cationic surfactant containing amide group: Batch adsorption experiments and Multiwfn wave function analysis.

The novel environment-friendly hexadecanoamide propyltrimethy lammonium chloride (NQAS16-3) surfactant with different amounts (0.2, 0.4, 0.6, 0.8, 1.0, 1.2 CEC) was firstly used to modify montmorillonite, and the obtained organomontmorillonite (N-Mt) with the amount of surfactant equal to 1.0 CEC was utilized to adsorb two ß-blocker pollutants- Atenolol (ATE) and acebutolol (ACE). The experimental results indicated that the equilibrium adsorption capacity of N-Mt(the organo-montmorillonite that the amount of modifier was 1.0 CEC) for ATE and ACE was 93.47 mg/g and 84.55 mg/g, respectively, which was more than twice that of raw montmorillonite for two pollutants, the adsorption was better fitted with the pseudo-second-order model and Langmuir isotherms model, and the adsorption was the spontaneous and exothermic process. Moreover, combining with the Zeta potential values of N-Mt, and with the help of Multiwfn wave function program based on density functional theory (DFT), the electrostatic interaction and the hydrophobic partitioning between N-Mt and two pollutant molecules were verified, p-π/π interaction between NQAS16-3 and ATE (or ACE) may be contributed to the increasing adsorption capacity of N-Mt for two ß-blocker pollutants. The work provided novel organomontmorillonite for the removal of non-degradable ß-blocker pollutants and the insight of the adsorption mechanism from the atomic level.

Exploration of adsorption mechanism of 2-phosphonobutane-1,2,4-tricarboxylic acid onto kaolinite and montmorillonite via batch experiment and theoretical studies.

Two clay minerals, kaolinite (Kaol) and montmorillonite (Mt) with different crystal structures were chosen to investigate the comparative adsorption of 2-phosphonobutane-1,2,4-tricarboxylic acid (PBTC) through batch control experiments and theoretical studies. The systematical isotherm and kinetic studies agreed with Langmuir model and pseudo-second-order model, confirming a monolayer and chemisorption interaction process, respectively. The maximum removal capacities of Kaol and Mt for PBTC were 72.297 mg/g and 121.163 mg/g at pH=3.0 and T=298 K, respectively. Furthermore, the adsorption mechanisms were investigated by molecular dynamic (MD) simulations and density functional theory (DFT). The Interface force field (IFF) was firstly introduced into Materials Studio package to explore the microscopic mechanism of clay mineral interface. The dynamics behaviors verified that the oxygen (O) atom of carboxyl group has stronger affinity at the external surface of Mt, which consistent with the experimental data well. For DFT calculations, quantitative analysis around molecular van der Waals (vdW) surface was adopted to predict reactive sites for the electrophilic reaction. Independent Gradient Model (IGM) and Hirshfeld surface analyses in Multiwfn indicated that the high adsorption effect mainly attributes to hydrogen bond action. These findings improve our ability to explore the related properties occurring at the interface of different clay minerals.

van der Waals potential: an important complement to molecular electrostatic potential in studying intermolecular interactions.

Electrostatics and van der Waals (vdW) interactions are two major components of intermolecular weak interactions. Electrostatic potential has been a very popular function in revealing electrostatic interaction between the system under study and other species, while the role of vdW potential was less recognized and has long been ignored. In this paper, we explicitly present definition of vdW potential, describe its implementation details, and demonstrate its important practical values by several examples. We hope this work can arouse researchers' attention to the vdW potential and promote its application in the studies of weak interactions. Calculation, visualization, and quantitative analysis of the vdW potential have been supported by our freely available code Multiwfn ( http://sobereva.com/multiwfn ).

Geometrical Structures and Electronic Properties of Ga6 and Ga5X (X = B, C, N, O, F, Al, Si, P, S, Cl) Clusters.

Based on the unbiased CALYPSO (Crystal structure Analysis by Particle Swarm Optimization) structure searching method in combination with density functional theory (DFT), the geometrical structures and electronic properties are investigated theoretically for Ga6 and Ga5X (X = B, C, N, O, F, Al, Si, P, S, Cl) clusters. The PBE0 exchange-correlation functional and the 6-311G(d) basis set is carried out to determine global minima on potential energy surfaces. The relative stabilities of the clusters are examined by the binding energies and substitution reaction. Following the predictions of the Jellium model, the Ga5B cluster with the 18 valence electrons is the most stable structure. At last, with the obtained lowest energy structures, some physical properties such as electrons transfer, molecular orbitals, and total and partial densities of states are discussed, respectively.