Atomic Charges Research Articles

Theoretical Analysis of Coordination Geometries in Transition Metal-Histidine Complexes Using Quantum Chemical Calculations.

A theoretical investigation utilizing density functional theory (DFT) calculations was conducted to explore the coordination complexes formed between histidine (His) ligands and various divalent transition metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, and Zn2+). Conformational exploration of the His ligand was initially performed to assess its stability upon coordination. Both 1:1 and 1:2 of metal-to-ligand complexes were scrutinized to elucidate their structural features and the relative stability of the complexes. This study examined the ability of His to act as a bidentate or tridentate coordinating ligand, along with the differences in coordination geometry when solvent effects were incorporated. The reduced density gradient (RDG) analysis and local electron attachment energy (LEAE) analysis were employed to elucidate the interaction planes and the nucleophilic and electrophilic properties. The electronic properties were analyzed through electrostatic potential (ESP) maps and natural population analysis (NPA) of atomic charge distributions. This computational study provides valuable insights into the diverse coordination modes of His and its interactions with divalent transition metal ions, contributing to a better understanding of the role of this amino acid ligand in the formation of transition metal complexes. The findings can aid in the design and construction of self-assembled structures involving His-metal coordination.

Investigation of Carbonation Kinetics in Carbonated Cementitious Materials by Reactive Molecular Dynamics Simulations.

Calcium carbonate (CaCO3) precipitation plays a significant role during the carbon capture process; however, the mechanism is still only partially understood. Understanding the atomic-level carbonation mechanism of cementitious materials can promote the mineralization capture, immobilization, and utilization of carbon dioxide, as well as the improvement of carbonated cementitious materials' performance. Therefore, based on molecular dynamics simulations, this paper investigates the effect of Si/Al concentrations in cementitious materials on carbonation kinetics. We first verify the force field used in this paper. Then, we analyze the network connectivity evolution, the number and size of the carbonate cluster during gelation, the polymerization rate, and the activation energy. Finally, in order to reveal the reasons that caused the evolution of polymerization rate and activation energy, we analyze the local stress and charge of atoms. Results show that the Ca-Oc bond number and carbonate cluster size increase with the decrease of the Si/Al concentration and the increase of temperature, leading to the higher amorphous calcium carbonate gel polymerization degree. The local stress of each atom in the system is the driving force of the gelation transition. The presence of Si and Al components increases the atom's local stress and average charge, thus causing the increase of the energy barrier of CaCO3 polymerization and the activation energy of carbonation.

Upgrading Electrolyte Antioxidant Chemistry by Constructing Potential Scaling Relationship.

Rational design of advanced electrolytes to improve the high-voltage capability has been attracting wide attention as one critical solution to enable next-generation high-energy-density batteries. However, the limited understanding of electrolyte antioxidant chemistry as well as the lack of valid quantization approaches have resulted in knowledge gap, which hinders the formulation of new electrolytes. Herein, we construct a standard curve based on representative solvation structures to quantify the oxidation stability of ether-based electrolytes, which reveals the linear correlation between the oxidation potential and the atomic charge of the least oxidation-resistant solvent. Dictated by the regularity between solvation composition and oxidation potential, a (Trifluoromethyl)cyclohexane-based localized high-concentration electrolyte dominated by anion-less solvation structures was designed to optimize the cycling performance of 4.5 V 30 μm-Li||3.8 mAh cm-2-LiCoO2 batteries, which maintained 80 % capacity retention even after 440 cycles. The consistency of experimental and computational results validates the proposed principles, offering a fundamental guideline to evaluate and design aggressive electrochemical systems.

Bidentate mode coordinated Ti3CNTx MXene-controlled interfacial engineering enables high-performance indoor organic photovoltaic devices

Two-dimensional MXenes demonstrate exceptional optoelectronic properties and tunable surface terminations, making them highly desirable materials for advanced organic photovoltaic (OPV) devices in indoor settings. This study introduced a solution-processed hybrid hole-transport layer (HTL) composed of a blend of 2-(9H-carbazol-9-yl)ethyl]phosphonic acid and titanium carbonitride (2PACz–Ti3CNTx). Introducing Ti3CNTx into 2PACz enhanced the work function for improved hole transport and also induced molecular alignment and interface dipole changes via formation of Ti–O–P covalent bond. This synergistic interaction led to atomic charge polarization, improving the hole-transport kinetics at the heterointerface of 2PACz and Ti3CNTx. Furthermore, the large surface area of conductive MXene and its chemical interaction with π-conjugated 2PACz promote the conductivity and charge-transfer pathways, improving the device’s performance. Consequently, OPV devices employing 2PACz–Ti3CNTx HTLs achieved the maximum power conversion efficiency of 30.3 % under a light-emitting diode lamp (1000 lx) and an output power density of 413 µW·cm−2 under a halogen lamp (1000 lx), corresponding to enhancements of approximately 16 % and 12 %, respectively, compared to OPV devices based on undoped HTLs. These results highlight new opportunities for further exploration of MXene compositions in high-performance indoor OPV devices.

Detailed investigation on FAME capped metal nanocomposite synthesis as potential antifungal agent

Oleaginous yeast lipid derived fatty acid methyl esters (FAMEs) are renowned for their exceptional potential towards bioenergy production specially in biodiesel domain. FAME application in other realms of biotechnology including nanotechnology (offer large possibilities for industry and contemporary science) has hitherto remained unexplored. Present study has investigated the novel use of FAME as biogenic capping agents to synthesize amphotericin B loaded CuO-CT (CT: chitosan) nanocomposites. The utilization of FAME-modified formulation (CuO-CTY@.L.F-AmpB) is evident in providing steric stability, as indicated by various physiochemical characterization techniques, accompanied by a low polydispersity index 0.24 ± 0.06 and a partial negative surface charge. Additional insights from HRTEM reveal a nanocarrier with a rod-shaped morphology, featuring 40–50 nm length and a 5–6 nm diameter. Amphotericin B release from CuO-CT@Y.L.F-AmpB followed a sustained pattern for up to 100 h, suggested FAME coating facilitated the drug release for a longer time duration. FAME stabilization has improved antibiofilm activity against Candida albicans (BEC50: 15 μg/mL) evinced by multitude assays that were found concordant with each other. A comprehensive FAME profiling conducted through GC-MS unveiled the predominance of oleic (84.02 ± 0.30 %) and palmitic acid methyl esters (9.40 ± 0.15 %) in the sample. This observation identifies them as concealed factors contributing to the stability of the nanocomposite. Conclusively, present study stipulated FAME as an efficient capping agent where it impart stability as well as efficacy to the nanocarrier. Moreover, current research work opens an innovative path for biorefinery approach integrating simultaneous production of lipid and multiphase nano-material synthesis, vital for a sustainable and circular bio-economy.

A polarizable valence electron density based force field for high-energy interactions between atoms and molecules.

High-accuracy molecular force field models suited for hot gases and plasmas are not as abundant as those geared toward ambient pressure and temperature conditions. Here, we present an improved version of our previous electron-density based force field model that can now account for polarization effects by adjusting the atomic valence electron contributions to match abinitio calculated Mulliken partial charges. Using a slightly modified version of the Hohenberg-Kohn theorem, we also include an improved theoretical formulation of our model when applied to systems with degenerate ground states. We present two variants of our polarizable model, fitted from abinitio reference data calculated at CCSD(T)/cc-pVTZ and CCSD(T)/CEP-31G levels of theory, that both accurately model water dimer interaction energies. Further improvements include the additional interaction components with fictitious non-spherically symmetric, yet atom-centered, electron densities and fitting the exchange and correlation coefficients against analytical expressions. The latter removes all unphysical oscillations that are observed in the previous non-polarizable variant of our force field.

Crystal field anisotropy correlated charge disproportionation in Ruddlesden-Popper Sr3-xCaxFe2O7-δ perovskites

A series of Ca2+-doped Ruddlesden-Popper phase perovskites Sr3-xCaxFe2O7-δ (x = 0∼0.4) were synthesized. Strong asymmetric FeO6 octahedral distortion was confirmed at x = 0.2 owing to the anisotropic chemical pressure applied from preferable occupation of Ca2+ ion at Sr2 site. Unusual high-charged oxidation state of iron ion with enhanced p→d charge transfer was collectively evidenced by X-ray photoelectron spectroscopy and Mössbauer spectroscopy. Combined electron emission spectroscopy further revealed a narrowing of the surface band gap accompanied by an apparent lowering of the conduction band edge at x = 0.2. These observations can be explained by a nontrivial partial charge disproportionated (CD) regime: d5L + d5L → d5L1−n + d5L1+n, which reflects a significant correlation between anisotropic chemical pressure and CD ground state. The d5L1−n ground state, which dominates the conduction band, is largely stabilized by enhancing the d(Fe)-p(O) hybridization along the c-axis. In addition, abrupt changes in both magnetism and dc electrical properties were also observed at x = 0.2. It is believed that the anisotropic crystal field correlated electronic state fluctuation of iron may facilitate magnetic phase competition and carrier transport. This work provides a comprehensive understanding of the crystallographic anisotropy and correlated valence electron behavior in Fe-base Ruddlesden-Popper perovskites, as well as quasi two-dimensional perovskite materials.

A theoretical study on dopants substituted on the H-terminated surface regulating the threshold concentration of nitrogen for accelerating diamond growth

Nitrogen is widely believed to accelerate the diamond growth by chemical vapor deposition (CVD). While there is currently no consensus on the reaction mechanism of nitrogen increasing the growth rate of CVD diamond. In this work, we have proposed a chemical adsorption model formed by substitutional nitrogen on the H-terminated surface of diamond. The first principles calculations based on density functional theory are used to systematically study the effects of substitutional nitrogen on several key features (i.e., surface absorption energy, geometric structure, atomic charge, electron bond population, and electron density) of the H-terminated surfaces. The results indicate that nitrogen substituted on the H-terminated surface are probably more favorable for hydrogen desorption, which can not only affect the properties of directly bonding adjacent species, but also cause changes in the geometric and electronic properties around the surface by electron transfer or forming additional covalent bonds. Furthermore, compared with single nitrogen doping, the co-doped structures formed by adding boron or phosphorus at a relatively low N/H ratio on the H-terminated surface could enhance or weaken the stability of the diamond surface, that is, weaken or enhance the desorption process of hydrogen. It is therefore proved the existence of a regulatory effect on the threshold concentration required for nitrogen to accelerate diamond growth.

HessFit: A Toolkit to Derive Automated Force Fields from Quantum Mechanical Information.

In this study, we introduce a novel approach to enhance the accuracy of molecular dynamics simulations by refining the force fields (FFs) through a combination of transferable parameters and molecule-specific characteristics derived from quantum mechanical (QM) calculations. Traditional FFs often prioritize generality over precision, leading to limitations in the accuracy of accurately capturing intra- and intermolecular interactions. To address this, we present an open-source toolkit, called HessFit, designed to integrate QM-derived bonded parameters and atomic charges into existing FFs. In combination with bond, angle, torsional, and nonbonded parameters derivation, HessFit can easily extract multiple barrier terms of dihedrals from QM Hessian and gradient or return all terms through a fitting procedure scheme of QM potential energy surface. We showcase the effectiveness of HessFit through comprehensive evaluations of vibrational properties across a diverse set of small molecules and demonstrate that experimental results support its ability in predicting thermodynamic properties of organic molecules compared to previous state-of-the-art approaches. We further explore its application to Zn2+ metalloprotein models, which are hard systems to treat with automatic approaches. Our results demonstrate that HessFit parameters compete with GAFF2 and OPLS parameters to describing small organic molecules, and its feasibility is also comparable to current FFs used to modeling nonstandard residues in Zn proteins for molecular dynamics simulations. The effectiveness of the HessFit protocol makes it a valuable tool for deriving or extending force field parameters for novel compounds in several molecular modeling applications.

3-Pyrazolyl-pyran-2-one: Synthesis, crystal structure, Hirshfeld surface analysis, DFT and ADME studies

Synthesis, crystal structure, Hirshfeld surface analysis, DFT and in-silico studies were carried out for the 4‑hydroxy-6-methyl-3-(1-phenyl-1H-pyrazol-3-yl)-2H-pyran-2-one 2. The reaction efficiency was evaluated performing two conditions to prepare the Vilsmeir-Haack reagent: phosphoryl trichloride in DMF and phosphorus pentachloride in DMF. The molecular structure was confirmed by 1H and 13C NMR, IR spectroscopy and X-ray diffraction analysis. The pyrazole and pyran rings are nearly coplanar. The molecules are connected through C—H···O hydrogen bonds, C—H⋯π and π⋯π stacking interactions, forming layers in the crystal lattice. Hirshfeld surface analysis for crystal packing indicates that the most important contributions are H⋯H (41.6 %), C⋯H/H⋯C (22.6 %), O…H/H…O (20.9 %) interactions. The frontier molecular orbital, Mulliken and QTAIM atomic charge, Molecular Electrostatic Potential, Natural Bond Orbitals were produced using the optimized structure by B3LYP/6–311G(d,p) level of theory. The calculated LUMOHOMO gap (4.261 eV) indicated that the eventual charge transfer and showed chemical reactivity. Intrinsic reaction coordinate (IRC) calculation confirm that the transition state connects the reactants to the products. The experimental geometry parameters of the title compound are compared with the geometry of the optimized molecule in the gas phase and found in good agreement. The crystal structure was further explored to define the interaction energy between the molecular pairs. The ADME profile that pyrazolyl-pyran-2-one 2 is an inhibitor of CYP1A2 one of the five key cytochrome isoforms enzymes involved in drug metabolism.

Enhancement of alkaline water-oxidation activity for amorphous CoOx by the underlying remote-region atom seeding

Scaling up hydrogen production via large-current-density water electrolysis requires durable electrocatalysts of oxygen evolution reaction (OER) to reduce energy consumption. While amorphous metal oxides are promising OER catalysts, the surface-sites-electronic-orbital chance from the underlying remote-region atom seeding remains elusive. Herein, vanadium atom was controllable seated in the underlying remote region of the bulk materials as a typical coupling mode of amorphous-CoVOx-supported amorphous CoOx (CoVOx@CoOx), to study long-distance atoms correlation. XPS characterization for CoVOx@CoOx can't reveal the V signal due to the limited test depth of 5 nm, suggesting that V is existent in the internal region where it can be detected by EDS with 1 μm test depth. For surface-etched CoVOx@CoOx, V XPS signal appeared due to the exposure of CoVOx counterpart. The bionic flower structured, amorphous CoVOx@CoOx presents low overpotential of 338.5 mV at an extremely high current density of 1000 mA cm−2 in 1 M KOH and reserves 90.4% of the initial catalytical current after 24 h operation, significantly outperforming single amorphous CoOx. Density functional theory calculations evidence that the charge transfer from V atoms of CoVOx to surface active Co sites of CoOx part leads to the d-band center of Co-3d orbital shifted towards the Fermi level, which enhanced O adsorption effect thus promoting the OER activity. This research not only provides an ultrahigh-current-tolerance OER catalyst but also throws in-depth insight into the long-distance atoms charge interaction towards knowledge-guide catalyst construction for practical utilization.

Synthesis, spectroscopic characterization, biological evaluation studies on 6-methoxy-8-nitroquinolinium picrate: A potent lung cancer drug

The compound 6-Methoxy-8-Nitroquinolinium Picrate was synthesized and characterized using FT-IR, FT-Raman, and UV–Vis spectroscopic techniques. Vibrational wavenumbers were calculated and compared with experimental values, while UV–Vis analysis revealed electronic transitions within the molecule. Frontier molecular orbitals, molecular electrostatic potential surface, Mulliken atomic charge distribution, and Natural bond orbitals analyses confirmed the molecule's bioactivity and validated the intramolecular charge transfer within the molecule. Antibacterial testing exhibited activity against Klebsiella pneumoniae, while in vitro cytotoxicity experiments demonstrated higher inhibition of A549 cancer cell lines compared to HeLa cell lines. Molecular docking supported the in vitro cytotoxicity findings, suggesting the potential for developing new lung cancer treatments based on this research.

Synthesis, crystal structure, spectroscopic characterization, in vitro, molecular docking and DFT studies of 1- (Tert-Butyl) 2-methyl (2S, 4R)-4-hydroxy pyrrolidine-1,2-dicarboxylate

A chiral pyrrolidine-based compound, namely 1-(Tert-Butyl) 2-Methyl (2S, 4R)-4-Hydroxy Pyrrolidine-1,2-Dicarboxylate (NHP), was synthesized and crystallized by the slow evaporation technique. NMR, FT-IR, ESI-MS, UV–visible spectroscopy, and elemental analysis designate the molecule. The molecule crystallized in the orthorhombic space group P212121, identified by X-ray diffraction (XRD). Quantum chemical calculations were performed using DFT at the B3LYP/6–311++G (d,p) level. The DFT-calculated optimal structural parameters and the XRD-derived parameters showed a good correlation. The frequency of NHP is calculated using the DFT method and compared with observed results. The synthesized compound's molecular reactivity was further investigated using Mulliken atomic charges, HOMO-LUMO, and molecular electrostatic potential (MEP). The molecule was tested for molecular docking with bio-enzymes such as α-amylase (1HNY) and cyclooxygenases (1PGG & 4COX). The compound showed 7 hydrogen bonding interactions with 1HNY and 8 hydrogen bonding interactions with 4COX. The DFT investigations strongly support the molecular docking results. The molecule's in-vitro anti-inflammatory and anti-diabetic activity was compared with conventional medication. The NHP showed superior anti-inflammatory activity with protein denaturation technique than the standard diclofenac sodium. The results showed that the molecule outperformed the conventional medication in tests for inflammation.

The Promising Potential of Cold Atmospheric Plasma Therapies

The outstanding properties and chemistry of cold atmospheric plasma (CAP) are not sufficiently understood due to their relatively complex systems and transient properties. In this paper, we tried to present a detailed review of the applications of CAP in modern medicine, highlighting the biochemistry of this phenomenon. Due to its unique characteristics, CAP has emerged as a promising tool in various medical applications. CAP, as a partially—or fully ionized—gas-retaining state of quasi-neutrality, contains many particles, such as electrons, charged atoms, and molecules displaying collective behaviour caused by Coulomb interactions. CAP can be generated at atmospheric pressure, making it suitable for medical settings. Cold plasma’s anti-microbial properties create an alternative method to antibiotics when treating infections. It also enhances cell proliferation, migration, and differentiation, leading to accelerated tissue regeneration. CAP can also be a powerful tool in anti-tumour therapies, stem cell proliferation, dental applications, and disease treatment, e.g., neurology. It is our belief that this article contributes to the deeper understanding of cold plasma therapy and its potential in medicine. The objective of this study is to demonstrate the potential of this relatively novel approach as a promising treatment modality. By covering a range of various biomedical fields, we hope to provide a comprehensive overview of CAP applications for multiple medical conditions. In order to gain further insight into the subject, we attempted to gather crucial research and evidence from various studies, hopefully creating a compelling argument in favour of CAP therapy. Our aim is to highlight the innovative aspects of CAP therapy where traditional methods may have limitations. Through this article, we intend to provide a convenient reference source for readers engaged in the examination of CAP’s potential in medicine.

Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains.

The current practical "workhorses" of the atomistic implicit solvation─the Poisson-Boltzmann (PB) and generalized Born (GB) models─face fundamental accuracy limitations. Here, we propose a computationally efficient implicit solvation framework, the Implicit Water Multipole GB (IWM-GB) model, that systematically incorporates the effects of multipole moments of water molecules in the first hydration shell of a solute, beyond the dipole water polarization already present at the PB/GB level. The framework explicitly accounts for coupling between polar and nonpolar contributions to the total solvation energy, which is missing from many implicit solvation models. An implementation of the framework, utilizing the GAFF force field and AM1-BCC atomic partial charges model, is parametrized and tested against the experimental hydration free energies of small molecules from the FreeSolv database. The resulting accuracy on the test set (RMSE ∼ 0.9 kcal/mol) is 12% better than that of the explicit solvation (TIP3P) treatment, which is orders of magnitude slower. We also find that the coupling between polar and nonpolar parts of the solvation free energy is essential to ensuring that several features of the IWM-GB model are physically meaningful, including the sign of the nonpolar contributions.

Adsorption Behaviour of Pb and Cd on Graphene Oxide Nanoparticle from First-Principle Investigations.

Graphene oxide (GO) is considered as a promising adsorbent material for the removal of metal from aqueous environments. Here, we have used the density functional theory (DFT) approach and a combination of parameters to characterise the interactions of GO with lead (Pb) and cadmium (Cd), i.e., typical harmful metals often found in water. Our model systems consist of a singly and doubly adsorbed neutral (Pb0, Cd0) and charged (Pb2+, Cd2+) atoms adsorbed on the GO nanoparticle of the chemical formula C30H14O15. We show that a single charged metal ion binds more strongly than a neutral atom of the same type. Moreover, to determine the possibility of multiple adsorptions of the GO nanoparticle, two metal atoms of the same species were co-adsorbed on its surface. We found a site-dependent adsorption energy such that when two atoms of the same specie are adsorbed at sites Si and Sj, the binding energy per atom depends on whether one of the two atoms is adsorbed firstly on the Si or Sj sites. Furthermore, the binding energy per atom for the two co-adsorbed atoms of the same specie (i.e., neutral or charged) is less than the binding energy of a singly adsorbed atom. This suggests that atoms may become less likely to be adsorbed on the GO nanoparticle when their concentration increases. We adduce the origin of this observation to be interplay between the metal-metal interaction on the one hand and GO-metal on the other, with the former resulting in less binding for the charged adsorbed metals in particular, due to repulsive interaction between two positively charged ions. The frontier molecular orbitals analysis and the calculated global reactivity descriptors of the respective GO-metal complexes revealed that all the GO-metal complexes have a smaller HOMO-LUMO gap (HLG) relative to that of pristine metal-free GO nanoparticle. This may indicate that although the GO-metal complexes are stable, they are less stable compared to metal-free GO nanoparticles. The negative values of the chemical potentials obtained for all the GO-metal complexes further confirm their stability. Our work differs from previous experimental studies in that those lacked details of the interaction mechanisms between GO, Pb and Cd, as well as previous theoretical studies which used limited numbers of parameters to characterise the GO-metal interactions. Rather, we present a set of parameters or descriptors which provide comprehensive physical and electronic characterisation of GO-metal systems as obtained via the DFT calculations. These parameters, along with those reported in previous studies, may find applications in rational design and high-throughput screening of graphene-based materials for water purification, as an example.

Theoretical studies for the detailed electronic structure of organotin(IV) derivatives of 4-fluoroanthranilic acid, X-ray structure of n-dibutyltin bis(4-fluoroanthranilate)

The present study describes the detailed DFT-based electronic structure calculations without any symmetry constraints being performed on di- and triorganotin derivatives of 4-fluoroanthranilic acid (AFA), viz. Me2SnL2 (1), n-Bu2SnL2 (2), Me3SnL (3), and Ph3SnL (4) (where L= monoanion of AFA). The structural and atomic charge analysis have confirmed the previously reported our experimental results, i.e. bicapped tetrahedral and distorted tetrahedral geometry for di- and triorganotin derivatives, respectively, and all the complexes 1–4 contain a positively charged central tin atom surrounded by a negatively charged system. The single crystal X-ray structure of complex 2 (n-Bu2SnL2) also suggests that AFA acts as a monoanion and bidentate ligand resulting a bicapped tetrahedral environment around tin. Various population analysis such as Mulliken (MPA), Hirshfeld (HPA), and natural population analysis (NPA) have been employed to calculate the charges at all the atoms. A finite difference approximation method has been used to explain the charge distribution within the studied complexes 1–4 based on the conceptual global and local reactivity DFT-based descriptions, frontier molecular-orbital analysis (FMOA), and molecular electrostatic potential maps (MEP). Further, the conceptual DFT-based global reactivity descriptors and frontier molecular orbital analysis show that the interactions between CT-DNA and complexes 1–4 may be groove binding or electrostatic. The integral equation formalism-polarizable continuum model (IEF-PCM) has been employed to calculate the UV–visible spectra of 1–4 in the solvent field, whereas the same in the gas phase has been obtained with the help of time-dependent DFT (TD-DFT) at the same level of theory. The intramolecular charge distribution in 1–4 has been investigated with the help of natural bond orbital (NBO) analysis. The topological and energetic parameters at the selected bond critical points in the coordination sphere of complexes 1–4 have been calculated using atoms-in-molecules (AIM) theory. The analysis of different kinds of non-covalent interactions (NCI) in complexes 1–4 has also been investigated.

Enhancing thermoelectric efficiency of benzodithiophene-thienothiophene copolymers through doping-induced charge transfer

Organic thermoelectric materials have been gaining increasing interest due to their capacity to convert waste heat into electricity. This study explores the impact of doping-induced charge transfer states on the thermoelectric properties of benzodithiophene-thieno[3,2-b]thiophene-based polymers (PBDTTT) doped with 2,3,5,6-Tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ). Detailed structural, optical, and electrical analyses were conducted on two specific polymers, PBDTTT:C (P1) and PBDTTT:EFT (P2). The investigation revealed distinct doping behaviors: P1 formed a partial charge transfer (PCT) complex, whereas P2 predominantly formed an integer charge transfer (ICT) complex. This distinction is attributed to the inherent structural differences and varying aggregation capabilities of the polymers. As a result, P2 exhibited enhanced electrical conductivity and a superior thermoelectric power factor compared to P1. This study emphasizes the critical role of polymer aggregation and charge-transfer mechanisms in optimizing the thermoelectric performance of conjugated polymers. It offers valuable insights for the development of efficient thermoelectric materials and the advancement of energy conversion technologies.

Hexa-peri-hexabenzocoronene as a vector sensing and delivery of Carmustine anticancer drug: A density functional theory study

We conducted research on the adsorption of carmustine (BCNU) on the surface of pristine, N-doped, and BN-doped Hexa-peri-hexabenzocoronene (HBC) nanographene using density functional theory calculations. We used the B3LYP functional in conjunction with 6-31+G(d) and 6-311+G(d,p) basis sets to perform geometrical optimization calculations, vibrational frequencies, and natural bond orbitals (NBO) analysis. The dispersion correction term of Grimme-D3 was incorporated to account for the dispersion interactions. We found that the geometry of the nanographenes remains unchanged after the drug molecule adsorption. The calculated adsorption energies (Eads) were −17.1 kcal.mol−1 for HBC-BCNU, −17.0 kcal.mol−1 for NHBC-BCNU, and −17.9 kcal.mol−1 for BNHBC-BCNU when using the 6-31+G(d) basis set. The corresponding values calculated employing the 6-311+G(d,p) basis set were −17.9, −17.3, and −19.1 kcal.mol−1, respectively. Analysis of frontier molecular orbitals (HOMO and LUMO) showed that the electronic properties of NHBC were significantly affected by the presence of BCNU. We used NBO analysis to investigate the distribution of partial atomic charges in different systems. Finally, using the transition state equation and the smaller basis set, we found that the required time for BCNU to release from HBC, NHBC, and BNHBC is approximately 3.3, 1.8, and 13.0 s, respectively. The obtained values are 13.0, 4.6, and 96.0 s, respectively, for the higher level of calculations. The recovery time for all nanographenes is within a reasonable range, while NHBC exhibits the highest sensitivity for drug detection.

SARS-CoV-2: Prediction of critical ionic amino acid mutations

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that caused coronavirus disease 2019 (COVID-19), has been studied thoroughly, and several variants are revealed across the world with their corresponding mutations. Studies and vaccines development focus on the genetic mutations of the S protein due to its vital role in allowing the virus attach and fuse with the membrane of a host cell. In this perspective, we study the effects of all ionic amino acid mutations of the SARS-CoV-2 viral spike protein S1 when bound to Antibody CC12.1 within the SARS-CoV-2:CC12.1 complex model. Binding free energy calculations between SARS-CoV-2 and antibody CC12.1 are based on the Analysis of Electrostatic Similarities of Proteins (AESOP) framework, where the electrostatic potentials are calculated using Adaptive Poisson-Boltzmann Solver (APBS). The atomic radii and charges that feed into the APBS calculations are calculated using the PDB2PQR software. Our results are the first to propose in silico potential life-threatening mutations of SARS-CoV-2 beyond the present mutations found in the five common variants worldwide. We find each of the following mutations: K378A, R408A, K424A, R454A, R457A, K458A, and K462A, to play significant roles in the binding to Antibody CC12.1, since they are turned into strong inhibitors on both chains of the S1 protein, whereas the mutations D405A, D420A, and D427A, show to play important roles in this binding, as they are turned into mild inhibitors on both chains of the S1 protein.