Solvent-accelerated photoreduction of Hg(II) dihalides: uncovering solvent-governed and light-triggered mercury chemistry.

A 3D-QSAR study using comparative molecular field analysis (CoMFA) was carried out on anti-tubulin agents with indole as a nucleus core. The structures of the compounds were obtained using docking calculations, and were then subjected to alignment procedures. CoMFA calculations for the 42 ligands that were examined as the training set gave a q2 value of 0.623 in correlation with experimental IC50 values for the inhibition of MKN-45 gastric cancer cells. Calculation for the test set of 17 ligands resulted in an r2 value of 0.714. The calculated results suggest that the R3 functional group site (see structure in Fig. 1) favored bulky groups while R1, R2, and R4 sites favored the opposite. At the R5 and R6 sites, parts of the region favored bulky groups while other parts favored the opposite. As for the electrostatic aspect, the R3 site was found to favor groups with a negative partial charge. At the R2 site, part of the region favored the group with a negative partial charge while other regions favored groups with a positive partial charge. The R4 and R5 sites favored groups with negative and positive partial charges, respectively, with a less favorable magnitude when compared with the R2 and R3 sites. The R1 and R6 sites did not exhibit significant electrostatic favor. Correlation of the results with IC50 values of ligands were analyzed and discussed.

Accurate information on the interactions between water and silica is critical to the understanding of its properties including mechanical strength under stress and long‐term chemical durability of silica and silicate glasses. In this study, interactions between water and nanoporous amorphous silica models were investigated using density functional theory ( DFT ) based ab initio molecular dynamics ( AIMD ) simulations which accurately describe bond breakage and formation as well as chemical reactions. AIMD simulations up to 30 ps were performed for systems containing water and nanoporous silica with a wide range of porosities (31%–67%). Partial removal of defects, such as two‐membered rings, was observed during the AIMD runs whereas more reactive coordination defects were removed during the initial geometry optimization. The limited two‐membered ring removal can be attributed to restricted water‐defect movement or the increased stability of rings located on concave surfaces. Two‐membered ring removal mechanisms included the formation of an overcoordinated silicon (Si 5 ) intermediate defect from the dynamic simulations. Si 5 defects continued to develop throughout the simulations, indicating a thermodynamic drive for two‐membered ring removal which is kinetically limited. Changes in the electronic structures, such as atomic charges, and bond length‐bond angle correlation functions were monitored during the hydroxylation process.

In this study, we extended the optimized potentials for liquid simulation-ionic-liquid virtual site (OPLS-VSIL) force field (FF) to imidazolium-based dicationic ionic liquids (DILs) and evaluated the ability of different OPLS-based FFs (i.e., OPLS-2009IL, 0.8*OPLS-2009IL, and OPLS-VSIL) in predicting different properties of the studied DIL by comparing their results with abinitio molecular dynamics (AIMD) simulation and experimental results. To achieve this purpose, MD simulations with three different OPLS-based FFs as well as AIMD simulation were performed for [C3(mim)2][NTF2]2 DIL and its structural, dynamical, vibrational, and volumetric properties were analyzed. Structural properties of the studied DIL, i.e., radial distribution functions (RDFs), structure factor, and hydrogen-bond network, showed that compared to 0.8*OPLS-2009IL FF, there is a much better agreement between the results of both OPLS-2009IL and OPLS-VSIL FFs with the AIMD simulation. On the other hand, the results of dynamical properties, such as mean square displacements, van Hove correlation functions as well as hydrogen bond, ion pair, and ion cage dynamics, depicted that in both 0.8*OPLS-2009IL and OPLS-VSIL FFs, the dynamics of the system is almost similar, and compared to OPLS-2009IL FF, they have better agreements with experimental results where they exist. So, it can be seen that although reducing the total charge of studied DIL by 20% leads to an increase in the dynamics of the system, the type distribution of partial charges on each atom does not significantly affect the system's dynamics. The calculated infrared (IR) and power spectra showed that the vibrational features of studied DIL in three OPLS-based FFs are mostly the same and reducing total charge and different type distribution of partial charges have no significant effect on the studied system. Furthermore, in volumetric properties, OPLS-VSIL FF shows somehow better agreement with experimental results. Overall, the evaluation of different structural, dynamical, vibrational, and volumetric properties of [C3(mim)2][NTF2]2 DIL shows that the OPLS-VSIL FF may be the best choice among the different studied OPLS FFs.

Tunable activity of electrocatalytic CO dimerization on strained Cu surfaces: Insights from ab initio molecular dynamics simulations

Interfacial chemistry involving glyoxal at aerosol surfaces is postulated to catalyze aerosol growth. This chemistry remains speculative due to a lack of detailed information concerning the physicochemical behavior of glyoxal at the interface of atmospheric aerosols. Here, we report results from high-level electronic structure calculations as well as both classical and Born-Oppenheimer ab initio molecular dynamics simulations of glyoxal solvation at the air/liquid water interface. When compared to the gas phase, the trans to cis isomerization of glyoxal at the liquid water interface is found to be catalyzed; additionally, the trans conformation is selectively solvated within the bulk to a greater degree than is the cis conformation. These two processes, i.e., the catalytic effect at the water interface and the differentially selective solvation, act to enhance the concentration of the cis isomer of glyoxal at the water interface. This has important consequences for the interpretation of experiments and for the modeling of glyoxal chemistry both at the interface of water clouds and at aerosols. Broader implications of this work relate to describing the role of interfaces in selecting specific stereo molecular structures at interfacial environments.

Si-based materials have recently drawn a great deal of attentions for their great promise to replace graphite as the anodes of Li-ion batteries. However, their use as the anodes are still suffering from the problems of poor durability and cycling performance during the lithiation and delithiation processes. One of the main reasons can be attributed to the fact that it cannot form a stable solid-electrolyte-interphase (SEI) layer on the lithiated silicon surface, thereby causing huge capacity loss during the electrochemical processes. Accordingly, a detailed atomistic understanding of the formation of SEI layers, particularly the reduction mechanisms of the electrolyte molecules on the anode surfaces, is of critical importance to help accelerate the realization of the Si-based anodes in Li-ion batteries. In this study, we employed first-principles density functional theory calculations and ab initio molecular dynamic (AIMD) simulations to investigate the reduction mechanisms of ethylene carbonate (EC) molecule on the amorphous lithiated surfaces of Si anodes in Li-ion batteries. We first generated the amorphous surface models of Si anodes within four different levels of lithiation (Li40Si88, Li64Si64, Li84Si44, and Li100Si28) via the MD “melt-and-quench” approach, and then examined the possible reduction pathways of EC molecules on these amorphous lithiated Si surfaces using ab initio molecular dynamic simulations. Our AIMD simulations showed that EC molecules can be reduced on the Li x Si surfaces via three different kinds of two-electron processes (two are simultaneous and one sequential), which appear to be highly dependent on the surface composition of the Si-based anodes. As the Li concentration on the anode surface was low (Li40Si88 and Li64Si64), our results showed that EC reduction was predominately initiated by the adsorption of a EC molecule onto the anode surface via the formation of Si-C bond followed by two simultaneous electron transfer leading to ring-opening, which can be represented using the following formula: EC + 2e- → OCOC2H4O2- (1) In this case, the interaction between the negatively charged surface Si atom and an EC molecule was found to be the main driving force to initiate this surface reduction reaction. However, on the highly lithiated Si surfaces (Li84Si44 and Li100Si28), the reduction of EC molecule was found to majorly proceed via another two simultaneous electron transfer process. In this reduction process, EC adsorption was driven by the electrostatic interaction between the C=O bond of an EC molecule and the positively-charged Li atoms on the anode surfaces. Moreover, our results showed that the reduction rate of EC decomposition tends to increase with the Li content on the anode surfaces, and the increment of EC reduction can be attributed to the enhanced electron transfer from the anode surfaces to the EC molecules as revealed in our work function calculations. Our calculations further showed that EC molecules can even go through a four-electron transfer process on these highly lithiated Si anode surfaces, leading to the formation of CO2- and O(C2H4)OCO2- products. Besides the mechanisms driven by adsorption, our AIMD simulations also revealed another reduction pathway on the highly lithiated Si surfaces via electron tunneling. In this case, the reduction of EC molecules can proceed via one sequential electron transfer process consisting of two steps: EC + e- → EC- (2) EC- + e- → CO3 2- + C2H4 (3) According to our prediction for the reaction energy, we found that this non-adsorption reaction was actually more energetically favorable than the reaction paths initiated by surface adsorption. However, it turns out to be an infrequent process on the lithiated Si surfaces due to its higher energy barriers to induce EC reduction. On the other hand, our calculations also showed that the reaction rate of EC reduction on the amorphous lithiated Si anode surfaces can be manipulated by some surface doping or chemical modification. These interesting new findings will also be addressed in this presentation.

Zeolitic Imidazolate Frameworks (ZIFs) are the new frontier in the field of metal-organic materials. They incorporate the confining properties of the more traditional aluminosilicate zeolites together with the catalytic activity provided by transition metal ions and organic links. Computation of atomic point charges for these hybrid materials is important in the field of molecular simulations for substantial prediction of experimental results. However, due to the structural complexity of advanced materials in general, studies involving derivation of point charges for these materials are truly scarce. In this article, we have derived the atomic point charges of ZIF-8 through fitting of the quantum electrostatic potential obtained systematically from density functional theory (DFT) calculations both on finite clusters of increasing size and on the periodic system. For the periodic system, fluctuations on the atomic charges have been studied through ab initio molecular dynamics simulations. Using the latter approach, we have extended the study to ZIF-2 and ZIF-3, where it has been found that charge fluctuations are, as well as for ZIF-8, very narrow, therefore justifying the use of the point charge approximation for these materials.

Based on MINDO/3 optimized geometries, molecular properties have been computed for lumiflavin and related methylated isoalloxazines. Excellent agreement with UV PES is obtained. Salient differences from previous work are identified in the interpretation of the spectra.Computed partial atomic charges are presented and discussed for both oxidized and reduced forms, including cationic and anionic species. The most polar portion of the isoalloxazine system is pyrimidine‐like ring C because of the high polarity of the carbonyl groups. Otherwise, N(1) and N(3) are the most negative ring atoms in the oxidized and reduced forms forms; C(4a) is also very negative in reduced forms. N(5) and N(10) are more negative in reduced than in oxidized forms. It is shown in two‐electron reduction that bond length changes are quite localized to the diazadiene portion of the molecule, but that changes in partial charges extend to rings A and B. Only the OCNHCO moiety does not experience much change in charge.Good correlation is obtained between MINDO/3 partial charges and proton NMR for both the aromatic and methyl protons on ring A, supporting the assignments by Grande and Müller. Also changes in 13C NMR spectra upon reduction are paralleled by changes in computed partial charges. The nature of two‐electron reduction is analyzed in terms of changes in HOMO/LUMO as well as geometry and charge distribution. A table of computed properties is included for all compounds studied: total energy, ΔHƒ, ionization potential, electron affinity, and dipole moment.

Influence of Mg2+, SO[formula omitted] and Na+ ions of sea water in crude oil recovery: DFT and ab initio molecular dynamics simulations

Synthesis of the first RNAs represents one of the cornerstones of the emergence of life. Recent studies demonstrated powerful scenarios of prebiotic synthesis of cyclic nucleotides in aqueous and formamide environments. This raised a question about their thermodynamic stability, a decisive factor determining their accumulation in a prebiotic pool. Here we performed ab initio molecular dynamics simulations at various temperatures in formamide and water to study the relative stabilities of the 2',3' and 3',5' isomers of cyclic nucleotides. The computations show that in an aqueous environment 2',3' cyclic nucleotides are more stable than their 3',5' counterparts at all temperatures up to the boiling point. In contrast, in formamide higher temperatures favor the accumulation of the 3',5' cyclic form, whereas below about 400 K the 2',3' cyclic form becomes more stable. The latter observation is consistent with a formamide-based origin scenario, suggesting that 3',5' cyclic nucleotides accumulated at higher temperatures subsequently allowed oligomerization reactions after fast cooling to lower temperatures. A statistical analysis of the geometrical parameters of the solutes indicates that thermodynamics of cyclic nucleotides in aqueous and formamide environments are dictated by the floppiness of the molecules rather than by the ring strain of the cyclic phosphodiester linkages.

Today, understanding the interaction between DNA molecule with nanoparticles and functionalized nanoparticles has a significant importance in medical applications and targeted drug delivery. Molecular dynamics simulation on double-stranded molecule with the structure of the double helix and sequence of (CCTCAGGCCTCC) was performed in three states. The aim was to evaluate the effect of gold nanoparticles (GNPs) with partial negative charge on the stability of a DNA molecule. During the simulation process, the GNPs become closed to the DNA molecule and phosphate groups of the DNA molecule guided the nanoparticles toward its major groove. At the end of the DNA molecule chain, the terminal nucleotide of the chain was laid flat on the surface of the GNPs due to excessive exposure to solvent molecules and occurrence of peeling and untwisting states. According to the results, proximity of the GNPs and functionalized GNPs to the DNA molecule led to increased configuration entropy. While conformational energy and van der Waals energy of the DNA molecule increased in the presence of the GNPs and functionalized GNPs, there was a reduction and an increase in the number of hydrogen bonds between complementary bases in the presence of the GNPs and functionalized GNPs, respectively. Radial distribution function was estimated for water molecules and sodium cations, compared to oxygen atoms of the phosphate group of the DNA molecule. Results were indicative of the release of water molecules from around the DNA molecule in the presence of the GNPs. In addition, the distance between sodium cations and the GNPs decreased. Nevertheless, no such phenomenon occurred in the presence of the functionalized GNPs. Therefore, according to results, it seems that GNPs decreased the stability of the DNA molecule and the functionalized GNPs with partial negative charge caused structural changes and created compression, but did not destroy the double-strand structure of the DNA molecule.

Ab initio restricted Hartree Fock and density functional theory (DFT), as well as semiempirical Austin model 1 and parametrization method 3 molecular orbital calculations were carried out for a range of chlorinated dioxin molecules to obtain molecular descriptors such as HOMO–LUMO gaps (HOMO = highest occupied molecular orbital, LUMO = lowest unoccupied molecular orbital) and partial atomic charges. The HOMO–LUMO gap is an indicator of stability in a molecule: the larger the gap the greater the stability of the molecule toward further reaction. These calculations indicate that with increasing extent of chlorination, the gap decreases. The observed charge pattern shows that carbon atoms in the peri (1,4,6,9) ring positions have a partial negative charge while those in the lateral (2,3,7,8) position have a partial positive or small partial negative charge. The descriptors, from the more precise DFT method, were used to rationalize experimental observations of dechlorination of dioxins. Reductive dechlorination pathways from two different experimental studies were examined using partial charges and estimated Gibbs free energy of dechlorination. In both experimental studies, highly thermodynamically favorable and less thermodynamically favorable pathways were observed. For a given chlorinated dioxin, when more than one degradation pathway was possible, dechlorination in the most thermodynamically favored pathway occurred at the most positively charged carbon atom in the ring, which was usually a lateral carbon atom. These results are discussed in light of a possible mechanism for reductive dechlorination.

Studies on the interaction between gold nanoparticles (AuNPs) and functional proteins have been useful in developing diagnostic and therapeutic agents. Such studies require a realistic computational model of AuNPs for successful molecular design works. This study offers a new multilayer model of AuNPs to address the inconsistency between its molecular mechanics' interpretation and AuNP's plasmonic nature. We performed partial charge quantum calculation of AuNPs using Au13 and Au55 models. The result showed that it has partial negative charges on the surface and partial positive charges on the inner part, indicating that the AuNP model should be composed of multiatom types. We tested the partial charge parameters of these gold (Au) atoms in classical molecular dynamics simulation (CMD) of AuNPs. The result showed that our parameters performed better in simulating the adsorption of Na+ and dicarboxy acetone in terms of consistency with surface charge density than the zero charges Au in the interface force field (IFF). We proposed that the multiple-charged AuNP model can be developed further into a simpler four-atom type of Au in a larger AuNP size.

Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of α-helices and antiparallel β-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Coulombic interactions

CO2 Capture via Crystalline Hydrogen-Bonded Bicarbonate Dimers