Atomic Charges Research Articles

Effect of Protein-Polarized Ligand Charges on Relative Protein Ligand Binding Affinities.

A major challenge in computer-aided drug design is predicting relative binding energies of different molecules to a target protein using fast and accurate free-energy calculation methods. Free-energy calculations are primarily computed by utilizing classical molecular dynamics simulations based on all-atom force fields (FF) to model the interactions in the system. The present standard classical all-atom FFs contain fixed partial charges on the atoms, and hence electrostatic interactions are modeled between them. The parametrization process to determine these partial charges usually relies on quantum mechanics or semiempirical calculations of the molecule in the gas phase or homogeneous water surrounding. These present standard parametrization schemes of the partial charges neglect, therefore, polarization effects from the protein surrounding. The absence of protein polarization effects can lead to significant errors in free-energy calculations in proteins. We present a parametrization scheme for the partial charges of ligands, named protein-induced polarization (PIP) charges, which account for the electrostatic polarization due to the protein surrounding. The scheme involves single-point quantum mechanics/molecular mechanics calculations of the ligand charges in the protein/water surrounding. Using PIP ligand partial charges, we have calculated the relative binding free energies (RBFEs) of well-studied protein-ligand systems. We show here that RBFEs computed with PIP charges are either significantly improved or at least comparable to those computed with nonpolarized standard GAFF charges. Overall, we present a simple-to-use parametrization scheme to include protein polarization in any type of binding free-energy calculations. The parametrization scheme increases the accuracy in RBFE calculations, while it does not add significant computation time to standard parametrization procedures.

Online Capacity Estimation for Lithium-Ion Batteries in Partial Intervals Considering Charging Conditions

Abstract Employed extensively for lithium-ion battery health assessment and capacity estimation, incremental capacity analysis (ICA) traditionally requires substantial time investment under standard charge and discharge conditions. However, in practical usage, Li-ion batteries rarely undergo full cycles. This study introduces aging temperature cycles within different partial intervals of the battery, integrating local ICA curves, peak range analysis, and incremental slope (IS) as an auxiliary feature. The extracted partial incremental capacity curves serve as features for state of health (SOH) estimation. The proposed temperature-rate-based SOH estimation method relies on a mechanistic function, analyzing relationships between temperature, different partial intervals, aging rate, and aging. Experimental tests on FCB21700 batteries demonstrate accurate SOH estimation using only partial charge curves, with an average error below 2.82%. By manipulating charging and discharging ranges, the method significantly extends battery lifespan, offering promising widespread applications.

Study on low-rank coal flotation collector screening and performance based on molecular polarity index.

Extensive studies using a trial-and-error approach have been conducted on low-rank coal flotation collectors. However, screening efficient collectors remains a considerable challenge due to the lack of suitable screening principles. It has proven that polar compounds such as carboxylic acids and esters are effective collectors for low-rank coal flotation. In this work, the effects of carboxylic acid, alcohol, and methyl ester on the floatability of low-rank coal were compared, the flotation performance of the polar collector was evaluated with theoretical calculations, a suitable evaluation parameter was determined and a screening principle based on this parameter was determined. The results show that the enhancement effects of polar collectors on low-rank coal floatability follow the order of methyl decanoate > methyl laurate > methyl octanoate > sec-octanol > methyl oleate (or methyl oleate > sec-octanol) > n-octanoic acid. Compared with the molecular polarity index, the hydrophobicity indices log P and dipole moment cannot be used to accurately evaluate different types of collectors and the same type of collectors, respectively. At room temperature, liquid polar compounds with molecular polarity indices in the range of 6.0 ~ 8.0kcal/mol effectively enhance the floatability of low-rank coal. The molecular polarity index of the collector is used for the first time to screen effective collectors of low-rank coal in this work. This parameter is anticipated to be highly important for the development and research of low-rank coal and other mineral collectors. To obtain reasonable and accurate molecular structure, geometry optimization and frequency calculations of the studied collectors were conducted via the Gaussian 09 software package based on density functional theory at the B3LYP/6-311 + G (d, p) level. The integral equation formalism for the polarizable continuum model (IEF-PCM) was utilized with water as the solvent (dielectric constant = 78.36, T = 298K) for all the calculations. Then, the atomic charge distributions (MPA and NPA) and electrostatic potential maps, the dipole moment and molecular polarity index, and the log P and water solubilities of studied collectors were shown or calculated by Gauss View 5.0, Mutiwfn program and website ( https://www.molsoft.com/mprop/mprop.cgi ), respectively.

Synthesis, characterization, DFT and molecular docking study of an antiviral drug, the crystallized 6-methoxylated derivative of favipiravir, in the presence of an iron (III) Lewis acid.

Few years ago, the COVID-19 infection, caused by SARS-CoV-2 virus, presented a worldwide health pandemic that taken the life of millions of people. In this concern, Favipiravir (FAV) has attracted considerable attention as an effective antiviral drug against this disease. In this study, the favipiravir's derivative (3‑hydroxy-6-methoxypyrazine-2-carboxamide) was synthetized, in presence of iron (III), and fully characterized through various analytical techniques including single-XRay, IR, UV and 1H/13C NMR. The refinement show the exclusive existence of enol form in the solid state. In solution, UV and NMR data were used to highlight the tautomeric equilibrium of this molecule. Additionally, the density functional theory (DFT) calculations were achieved to estimate the chemical parameters, electronic affinity and molecular electrostatic potential of the compound. Mulliken atomic charges as well as the chemical reactivity descriptors were investigated. Finally, the two tautomer forms of synthetized derivative were docked on SARS-CoV-2 main protease (PDB: 6LU7) and spike receptor-binding domain (PDB: 7BZ5) to evaluate their binding affinity. The docking simulation studies was predicted that the two forms had high binding affinity the critical amino acids residues of the receptor. This affinity was attributed to the presence of several hydrogen bonds for both tautomer along with five different hydrophobic interactions with the enol form. These results conduct to conclude that the synthetized product could be an interest potential drug for that type of diseases.

Capacity estimation of lithium-ion battery based on soft dynamic time warping, stratified random sampling and pruned residual neural networks

Accurate battery capacity estimation is crucial for ensuring battery management systems' safe and reliable operation. Although deep learning algorithms have been widely applied in the field of image recognition, their application in battery diagnosis is relatively limited. Besides, obtaining complete cycling data during charging/discharging processes can be challenging in practical applications. This paper proposes a battery capacity estimation method based on partial charge curves and pruned residual neural networks. To leverage the aging information inherent in partial charge curves, the partial segment battery data is transformed into images using wavelet denoising and soft dynamic time warping algorithms. Subsequently, we present a stratified random sampling method to address the issue of imbalanced sample distributions in battery dataset partitioning, and employ residual neural networks to mitigate performance degradation caused by stacking multiple network layers. To validate the effectiveness of the proposed method, experiments are conducted on three types of battery data. During the experimental phase, the root mean square error and mean absolute error of estimated battery capacity are both below 0.79% and 0.54%. Furthermore, a hybrid-pruning algorithm is proposed to enable the deployment of the model on the battery management system, which reduces the model size and computational complexity without compromising accuracy. Compared to other pruning algorithms, the proposed hybrid-pruning algorithm outperforms diagnostic accuracy and computational efficiency after fine-tuning, reducing the model size by 77.40% and creating a more compact structure.

Dressing a Nonpolarizable Force Field for OH- in TIP4P/2005 Aqueous Solutions with Corrected Hirshfeld Charges.

We present a rigid model for the OH- ion parametrized for binary mixtures with TIP4P/2005-type water molecules. Li+, Na+ and K+ were selected as counterions, hence mimicking the important and widely used solutions of soluble alkaline hydroxides. The optimized atomic charge distributions were obtained by scaling in a factor of 0.85 those derived from the atomic dipole corrected Hirshfeld approach. The agreement between experimental and Molecular Dynamics simulation results is remarkable for a set of properties, namely, the dependence of the density of the solutions on the hydroxide concentration and on temperature, the structure (i.e., positions of the atom-to-atom radial distribution functions and coordination numbers), the viscosity coefficients, the surface tension, or the freezing point depression. The proposed optimized potential parameters for OH- thus enlarge the set of models comprised within the Madrid-2019 force field and widen the potential applicability of the TIP4P/2005 water model in basic environments.

Comparative computational analysis of orthoconic antiferroelectric liquid crystals: DFT analysis.

The study undertakes a comparative analysis of four distinct semi-fluorinated chiral Organic Active Ferroelectric Liquid Crystals (OAFLCs). The comparative analysis of the compounds is done by using various parameters, including thermodynamic, non-linear optical, electrical, atomic charge distribution, and atomic orientations. We use optimization algorithms to look at chemical reactivity, electrical properties, intermolecular interactions, and static hyperpolarizability. Sample 4 is the best choice for a wide range of display applications. This research contributes to understanding the nuanced properties of semi-fluorinated chiral OAFLCs and highlights Sample 4's potential for novel applications in display technology, owing to its superior stability and optimized properties. This study helps to enhance our understanding of the comparative analysis of semi-fluorinated chiral OAFLCs for potential advancements in display technologies by incorporating findings from key studies. The simulations are performed using density functional theory (DFT) with the B3LYP functional for predicting molecular properties, and Vibrational Energy Distribution Analysis (VEDA) software is used to perform the vibrational analysis of the molecules.

MB38(M=Be and Zn): A Quasi-Planar Structure Rather Than a Core-Shell Octahedral Borospherene Structure.

In a recent paper (ChemPhysChem, 2023, 24, e202200947), based on the results computed using DFT method, the perfect core-shell octahedral configuration Be@B38 and Zn@B38 was reported to be the global minima of the MB38(M=Be and Zn) clusters. However, this paper presents the lower energy structures of MB38(M=Be and Zn) clusters as a quasi-planar configuration, the Be atom is found to reside on the convex surface of the quasi-planar B38 isomer, while the Zn atom tends to be attached to the top three B atoms of the quasi-planar B38 isomer. Our results show that quasi-planar MB38(M=Be and Zn) at DFT method have lower energy than core-shell octahedral configuration M@B38(M=Be and Zn). Natural atomic charges, valence electron density, electron localization function (ELF) analyses identify the MB38(M=Be and Zn) to be charge transfer complexes (Be2+B38 2-and Zn1+B38 1-) and suggest primarily the electrostatic interactions between doped atom and B38 fragment. The photoelectron spectra of the corresponding anionic structures were simulated, providing theoretical basis for future structural identification.

Diffusion mechanisms for spinel ferrite NiFe2O4 by using kinetic activation-relaxation technique.

Mass transport in bulk spinel ferrites NiFe2O4 is studied computationally using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo algorithm. Diffusion mechanisms-difficult to observe with molecular dynamics-are described by k-ART. Point defects are assumed to be responsible for ionic diffusion; thus, both cation and anion defects are investigated. This work focuses on vacancies and interstitials by comparing their properties with two Buckingham potential parameterizations: one with nominal charges and the other with partial charges. Both potentials are corrected at short distances, thus allowing interstitial diffusion and avoiding the catastrophic infinite energies appearing with Buckingham at short distances. The energy landscape along different pathways is described in detail. Both potentials predict the same mechanisms but different migration energies. Mechanisms by which a normal spinel is transformed to an inverse spinel via cation diffusion are unveiled, and diffusion coefficients are predicted. We find that interstitial Ni diffusion involves the movement of two Ni ions and that O interstitials trigger a collective diffusion of O ions, while an O vacancy diffuses by an O ion moving to the center of a cuboctahedron.

Design and synthesis of novel quinoxaline-piperazine linked isoxazole conjugates: Anti-cancer assessment, tyrosine kinase EGFR inhibitory activity, molecular docking and DFT studies

In this paper, we describe the synthesis of a novel series of quinoxaline-piperazine-isoxazole conjugates. We confirmed the structures of the newly synthesised compounds using 1HNMR, Mass, and 13CNMR spectroscopic techniques. The anti-tumour activity was evaluated on two human cancer cell lines, such as MCF-7 (breast) and A-549 (lung). The anti-cancer evaluation dates show that compounds 7f, 7e, and 7 g have more promising anti-cancer activity than the standard drug Erlotinib. We tested three potent compounds (7f, 7e, and 7 g) against a normal breast cell line in a cell survivability test (MCF-10A). Interestingly, none of them killed the cancer cells significantly (IC50 values greater than 88.91 µM). In addition, in vitro tyrosine kinase EGFR inhibitory activity has shown that compounds 7e and 7f display the highest tyrosine kinase EGFR inhibitory potency with an IC50 value of 1.10 and 0.85 µM, respectively, compared to the reference Erlotinib with an IC50 value of 1.24 µM. Furthermore, molecular docking analyses revealed that compounds (7f, 7e, and 7 g) exhibited a higher number of EGFR binding interactions. In this work 7f, the molecule was characterised by using density functional theory (DFT) with B3LYP/6–311G++ (d, p) basis set. The structural parameters were obtained from geometry optimization. Molecular electrostatic potential (MEP), HOMO-LUMO energy gap, and Mulliken atomic charges were calculated. The potent compounds 7f, 7e, and 7 g were subjected to in silico pharmacokinetic assessment by SWISS, ADME, and pkCSM. The three compounds (7e, 7f, and 7 g) intriguingly matched all four of the above-mentioned conditions exactly, with the exception of compound 7f's Ghose rule.

Electronic interaction and band alignment between Cu sub-nanometric clusters and ZnIn2S4 nanosheets towards selective photoreduction of CO2 to CO

Engineering the electronic properties of heterogeneous photocatalysts with charge transfer regulated is an effective strategy to boost their CO2 reduction activity. Here, we drew inspiration from the strong metal-support interaction effect, and fabricated ZnIn2S4 supported-Cu sub-nanometric clusters photocatalyst. Within this catalyst, the formed CuS bond would redistribute interfacial charge, resulting in diverse chemical states of Cu atoms and the establishment of Ohmic contact between ZIS and Cu. The built-in electric field of such Ohmic contact benefited the migration of photoexcited electrons from ZIS to Cu. Further mechanistic studies unveiled the crucial role of positively charged Cu atom near the interface in facilitating H2O dissociation, and its adjacent Cu atom at the top-surface adopting a distinct chemical state could activate linear CO2 molecule into a bent configuration. These features substantially lowered energy barriers for CO2 adsorption and subsequent *COOH formation, and Cu-ZIS, accordingly, exhibited a remarkable CO production rate of 60.2 μmol g-1h−1, approximately 20.8-fold enhancement compared to ZIS counterpart.

Novel coumarin-Schiff base derived electronically distinct fluorescent probes: Synthesis and comparative investigations of their unique selective sensing properties with Cu2+ and Cu+ ions

The present work describes the synthesis and comparative investigations of Cu2+ and Cu+ ions sensing properties of two novel π-extended coumarin-Schiff base-derived electronically distinct fluorescent probes (4 and 5). Due to the additional electron donating group substituent (-NEt2) close proximate to the binding site of Schiff base in probe 5, it exhibits distinct electronic properties compared to probe 4. Our studies indicate that probe 5 displays efficient and highly selective fluorescence quenching behaviors with Cu2+ and Cu+ ions compared to other competitive metal ions (Ca2+, Mg2+, Al3+, Hg2+, Pb2+, Cd2+, Mn2+, Co2+, Ni2+, Fe2+, Fe3+, Cr3+ and Zn2+). In our studies, Job's plot experiments revealed that the binding stoichiometry of the ligand-Cu2+ was 1:1 for both probes. The limit of detection (LOD) of 2.35 × 10–5 M and 1.56 × 10–5 M were obtained for the probes 4 and 5, respectively. Further, the Stren-Volmer equation has been used to calculate the binding abilities of probes with Cu2+ ions; it reveals the binding constant of 6.70 × 104 M-1 and 22.0 × 104 M-1 for probes 4 and 5, respectively. Also, in the present studies, our DFT computed results were comparatively presented to understand the electronic parameters (HOMO-LUMO energy band gaps, ESP and Mulliken atomic charge distribution) of compound 1, probes 4 and 5. We anticipate that the developed probes can be used to analyze Cu2+ and Cu+ ions in environmental and biological samples.

A Computational Analysis of the Proton Affinity and the Hydration of TEMPO and Its Piperidine Analogs.

The study investigated the impact of protonation and hydration on the geometry of nitroxide radicals using B3LYP and M06-2X methods. Results indicated that TEMPO exhibited the highest proton affinity in comparison to TEMPOL and TEMPONE. Two pathways contribute to hydrated protonated molecules. TEMPO shows lower first enthalpies of hydration (ΔH1-M), indicating stronger H-bonding interactions, while TEMPONE shows higher values, indicating weaker interactions with H2O. Solvent effects affect charge distribution by decreasing their atomic charge. Spin density (SD) is primarily concentrated in the NO segment, with minimal water molecule contamination. Protonation increases SD on N-atom, while hydration causes a more pronounced redistribution for water molecules. The stability of the dipolar structure (>N·+-O-) is evident in SD redistributions. The frontier molecular orbital (FMO) analysis of TEMPONE reveals a minimum EHOMO-LUMO gap (EH-L), enhancing the piperidine ring's reactivity. TEMPO is the most nucleophilic species, while TEMPONE exhibits strong electrophilicity. Transitioning from NO radicals to protonated forms increases the EH-L gap, indicating protonation stabilizes FMOs. Increased water molecules make the molecule less reactive, while increasing hydration decreases this energy gap, making the molecule more reactive. A smaller EH-L gap indicates the compound becomes softer and more prone to electron density and reactivity changes.

New hydrazide-hydrazone derivatives containing coumarin and indole moiety: Synthesis, spectroscopic characterization and DFT studies

Two new compounds (3 and 4), coumarin indole derivatives with a hydrazide-hydrazone skeleton, were synthesized, and their spesctroscopic properties, including UV-vis, FTIR, and 1H-13C NMR were investigated experimentally and theoretically. The experimental data and DFT (density functional theory) results of the compounds matched well and showed good agreement. Moreover, the DFT/B3LYP/6-311G++(2d,p) calculations were utilized to perform HOMO and LUMO energy, net atomic charges, MEP surface, and NBO analysis for the optimized geometries of 3 and 4. NBO analysis revealed that the synthesized compounds exhibit high molecular stability because of significant hyperconjugative interactions. The experimental and theoretical band gaps (ΔEg) investigated in some organic solvents with different polarities were determined to be in the range of 2.68-2.75 eV and 3.22-3.25 eV for compound 3, and 2.69-2.77 eV and 3.41-3.47 eV for compound 4, respectively. The compounds demonstrated thermal stabilities with a Td value higher than 300 °C.

Rosmarinic Acid as a Potential Multi-targeted Inhibitor for SAR-CoV-2: An In silico Virtual Screening Approach

Background: Rosmarinic acid, a natural compound found in various plants like rosemary and lemon balm, may have potential as a multi-targeted inhibitor for SARS-CoV-2, a strain of virus responsible for COVID-19. SARS-CoV-2, a fusion protein of S1 and S2 subunits, has multiple precursors angiotensin-converting enzyme2 (ACE2), transmembrane serine protease 2 (TMPRSS2), papain-like protease (PLpro), and 3-chymotrypsin-like protease (3CLpro). The chemical interaction of Rosmarinic acid with SARS-CoV-2 is of major interest reported here. Objective:: The quantitative study of Rosmarinic acid with various precursors of SARS-CoV-2 has been accounted for in detail. Furthermore, the conformational flexibility of Rosmarinic acid has also been investigated during the interaction with four different precursors of SARS-CoV-2. Methods: This investigation delves deeply into the analysis of various aspects, including geometric parameters, atomic charge, the energy gap between the highest occupied and lowest unoccupied molecular orbitals, dipole moments, and the analysis of non-covalent interactions (NCI). Furthermore, the study incorporates molecular docking techniques in conjunction with thorough quantum chemical calculations to provide comprehensive insights. Results: Rosmarinic acid shows promise as a versatile inhibitor of SARS-CoV-2, the virus responsible for COVID-19. It can target multiple key precursors of the virus, including TMPRSS2, angiotensin- converting enzyme2, 3CLpro, and PLpro, found in the fusion protein comprising S1 and S2 subunits. This study delves into the quantitative analysis of Rosmarinic acid's interactions with these precursors. Its adaptable structure allows it to engage with them effectively. Various molecular parameters, including atomic charge, energy gap between molecular orbitals, dipole moment, and noncovalent interactions, are comprehensively explored. Conclusion: Combining molecular docking and quantum mechanics, the findings suggest Rosmarinic acid's potential as a multi-targeted SARS-CoV-2 inhibitor.

A DFT Analysis of Structural and Electronic Features of [Mo(CO)6‐n(SiX)n] (n=1, 2 and 3, and X=O, S, Se and Te) Complexes

AbstractDFT was used to analyze the molecular and electronic structures of the mono, di‐ and tri‐substituted isomers of [Mo(CO)6‐n(SiX)n] (where, X=O, S, Se, Te) and they were compared to the Mo(CO)6 complex. The total energy of all the complexes indicates that the trans isomer is slightly more stable than the cis isomer, but the stability of the fac and mer isomers is comparable. The HOMO‐LUMO energy gap of the complexes was determined and it indicated that the energy gap of the newly designed complexes is smaller than that of the parent complex Mo(CO)6 (1), ranging from 3.45–5.08 eV for the complexes 2–21. The FMO analysis of 2–21 showed that they are more reactive than complex 1. Insights on the bonding nature of these complexes are provided by the NPA, NBO, and EDA studies. The bond contribution from the Si atom in the Mo−Si bond is greater than that from the Mo atom, based on the NBO study. However, the C atom contributes more to the Mo−CO bond as well. Atomic charges on the Mo atom have a higher negative charge and the Si atom shows a positive charge in all the complexes. This study provides valuable information about the isolobal and isoelectronic nature of different substitutions of Si−X bonds at different positions instead of CO molecule in [Mo(CO)6].

Investigation of spectroscopic characterization, crystal structure, and antitumor activity of a novel 2ATP molecule

In this section, the spectroscopic characteristics of 2-amino-toysl-pyridine (2ATP) are fully examined, using both experimental and computational investigations guided by density functional theory (DFT). It will facilitate our computational research using the B3LYP approach to use the basis set 6–311++G(d,p). Comprehensive assignments of vibrational modes were obtained from the vibrational spectra, which comprised FT-Raman and FT-IR spectroscopy and were recorded in the region of 3500–400 cm−1 and 4000–500 cm-1, respectively, using the Vibrational Energy Distribution Analysis (VEDA) approach. The net atomic charges inside the molecule were ascertained by using Mulliken population analysis, natural atomic charges, and electrostatic potentials (CHELPG). The structural conformations of 2ATP were determined using NMR spectroscopy in a CDCl3 solvent. The donor-acceptor interactions of the 2ATP molecule at the 6–311++G(d,p) level were studied by means of a Natural Bond Orbital (NBO) study. Studies of the ultraviolet (UV) spectrum in ethanol were used to assess the effects of the solvent. An assessment was made of the energy difference between the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO) in order to understand charge transfer processes that suggest the molecule may have biological activity. Molecular electrostatic potential (MEP) surfaces were used to predict the nucleophilic and electrophilic sites in molecules. The non-covalent interactions were evaluated using the reduced density gradient (RDG) approach. The Multiwfn software was used to analyze the topological properties of the 2ATP, including the Localized Orbital Locator (LOL) and Electron Localization Function (ELF). Further attention was drawn to the compound's exceptional pharmacological potential when its ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) characteristics were evaluated. Not to add, molecular docking experiments were carried out to evaluate the feasibility of 2ATP as a bioactive material with possible uses in the pharmaceutical business.

5-(Pyridin-3-yl)-3,4-dihydro-2H-furan-1-ium (NNKFI): a computational study of its physico-chemical properties.

Recent work on the diazonium ion metabolite of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNKDI) suggests that 5-(pyridin-3-yl)-3,4-dihydro-2H-furan-1-ium (NNKFI) may form from NNKDI via an intramolecular reaction. NNKDI is an important carcinogen whose role as an alkylating agent has received significant attention. While there is some experimental evidence supporting NNKFI's production in vitro, it has not yet been directly observed. Little is known about NNKFI's structure and reactivity. We report the first in silico examination of this ion. Our study utilized Kohn-Sham density functional theory (B3LYP/6-311G**) and coupled cluster theory (CCSD/6-31G*) to produce energy-optimized structures, vibrational normal modes and molecular orbitals for NNKFI. To gain insight into the chemical properties of this species, we calculated electrostatic potential surfaces, natural population analysis charges and local Fukui indices. We report data and results for NNKFI's cis and trans conformers. Our work confirms C5 as the preferred site for nucleophilic attack in NNKFI. Stretching motions and predicted bond lengths near O1 are consistent with a somewhat weakened carbonyl structure in this ion. Partial charges, electrostatic potential surfaces and local Fukui indices reveal delocalization of cationic charge on the furanium moiety and notable carbocation character at C5.

GMXPolymer: a generated polymerization algorithm based on GROMACS.

This work introduces a method for generating generalized structures of amorphous polymers using simulated polymerization and molecular dynamics equilibration, with a particular focus on amorphous polymers. The techniques and algorithms used in this method are described in the main text, and example input scripts are provided for the GMXPolymer code, which is based on the GROMACS molecular dynamics package. To demonstrate the efficacy of our method, we apply it to different glassy polymers exhibiting varying degrees of functionality, polarity, and rigidity. The reliability of the method is validated by comparing simulation results with experimental data in various structural and thermal properties, both of which show excellent agreement. This work implements the GMXPolymer simulated polymerization algorithm on the GROMACS program. GMXPolymer code controls the main polymerization loop. The energy minimizations and molecular dynamics simulations use the GROMACS program called by the GMXPolymer code. A new ITP file is generated when a new bond is formed, and the necessary additions to the ITP file are made to include new bonds, angles, and dihedrals. In preparing the ITP file of the monomer, the charge of the reactive atom must be modified before the code runs so that it is a correct value after bonding.

Diorganotin(IV) derivatives of ONO tridentate Schiff bases: Synthesis, spectroscopic characterization, DFT studies, CT-DNA binding, and plasmid-DNA cleavage studies

Two Schiff bases 2-amino-N'-(5‑bromo-2-hydroxybenzylidene)-3-(4-hydroxyphenyl)propanehydrazide (H2L1) and 2-amino-N'-(5‑chloro-2-hydroxybenzylidene)-3-(4-hydroxyphenyl)propanehydrazide (H2L2) and their six diorganotin(IV) complexes (R = C4H9 (1, 4), CH3 (2, 5), and C8H17 (3, 6)) have been synthesized. Schiff bases (H2L1–2) and their R2SnL1–2 complexes (1–6) have been characterized by CHNS analysis, IR spectroscopy, 1H, 13C, 119Sn NMR, and ES-MS. Schiff bases (H2L1–2) act as a dianionic tridentate ligand coordinated to Sn through phenolic and enolic oxygen and azomethine nitrogen in R2SnL1–2 complexes (1–6). A density functional theory (DFT)-based quantum chemical calculation validated the structures of R2SnL1 (1–3) and R2SnL2 (4–6) at the B3LYP/6‐311G(df,pd)/Def2‐SVP(Sn) and B3LYP/6‐31G(d,p)/Def2‐SVP(Sn) levels of theory, respectively. At these levels of theories, comprehensive electronic structure calculations determined atomic charges at selected atoms. Additionally, a molecular electrostatic potential (MEP) map identified electrostatic potential-varying sites on the molecule's surface, and MEP maps used to identify regions where other molecules might interact or react with the molecules on them. Furthermore, a conceptual-DFT-based global reactivity descriptor determined the stability and reactivity behaviour of R2SnL1–2 complexes (1–6). H2L1–2 and R2SnL1–2 complexes (1–6) have binding constants in the range ∼105 M-1 with CT-DNA, as revealed by UV–visible and fluorescence spectral titrations. UV-visible, fluorescence spectroscopy, and CD studies suggested that H2L1–2 and their R2SnL1–2 complexes (1–6) interact with CT-DNA electrostatically or groove-bound. DNA cleavage studies reveal that H2L1–2 and their R2SnL1–2 complexes (1–6) have ability to cleave the plasmid-DNA from its supercoiled form (SC, I) to nicked form (NC, II). However, n-Bu2SnL2 (4) and n-Oct2SnL2 complex (6) have higher cleavage activity than Schiff bases and other R2SnL1–2 complexes (1–6).