6-31G* basis set for atoms K through Zn

Electric Field Influence on CO Clathrate Hydrates

We consider carbon monoxide (CO) confined in the hydrogen-bonded building blocks of sI and sII clathrate hydrates, viz., (512, 51262, 51264) cages, within the density functional theory-based calculations. We study their response to the applied electric fields in terms of changes in the geometrical parameters, dipole moment, HOMO-LUMO gap, and vibrational frequency shift. We examine the stability of CO clathrate hydrate building block cages and identify a possible indication of the field-induced release of CO.

Thermal Decomposition of 2-Cyclopentenone

The thermal decomposition of 2-cyclopentenone, a cyclic oxygenated hydrocarbon that occurs in the pyrolysis of biomass, has been studied in a combined experimental and theoretical approach. Gas-phase pyrolysis was performed at temperatures ranging from 1000 to 1400 K in a pulsed, microtubular reactor. Products were identified by FTIR spectroscopy following their isolation in a low-temperature argon matrix. The following products were identified: carbon monoxide, ketene, propenylketene, vinylacetylene, ethylene, propene, acrolein, acetylene, propyne, and propargyl radical. Computational results identify three different decomposition channels involving a H atom migration, and producing prop-2-enylketene (Pathway 1), prop-1-enylketene (Pathway 2), and a second conformation of prop-2-enylketene (Pathway 3). A fourth decomposition pathway involves simultaneous rupture of two C-C bonds forming a high energy cyclopropenone intermediate that further reacts to form ethylene, acetylene, and carbon monoxide. Finally, a fifth pathway to the formation of acrolein and acetylene was identified that proceeds via a multistep mechanism, and an interconversion from 2-cyclopentenone to 3-cyclopentenone was identified computationally, but not observed experimentally.

Exploring Border Conditions for Spontaneous Emergence of Chirality in Allylboration of 1,2,3-Triazolic Aldehydes

A case of spontaneous chirality generation was observed during a synthetic project studying the allylboration of 1,2,3-triazolic aldehydes. Here, we present computational studies supported by experimental findings targeting the elucidation of border conditions required for the observation of spontaneous chirality generation in the reaction of 1-Ar-1H-1,2,3-triazole-4-carbaldehydes 1a,b with triallylborane. Three possible sources of symmetry breaking were found computationally. Thus, dimerization of the initial reaction products, alcoholates 4a,b, gives dimers 5a,b (homochiral) and 6a,b (heterochiral). The latter were computed to be more stable thermodynamically, which can lead to amplification of the initial stochastic imbalance of the enantiomers of 4a,b via the reservoir mechanism. Furthermore, enantiomeric excess can be increased during the transfer of the second allylic group in the reaction of optically active boronates 4a,b with 1a,b, which was computed to be enantioselective due to the strong activating and stereoregulating properties of the 1,2,3-triazole group. In addition, reactions of borinic esters 8a,b, products of the previous reaction with triallylborane, recovered in each case two molecules of 4a,b of the same handedness, which can lead to additional chirality amplification. Experimentally, reactions of optically active alcohols (+)-R-2a,b with triallylborane provided chiral alcoholates 4a,b, which were reacted with equivalent amounts of corresponding aldehydes 1a,b. Unexpectedly, in two series of 10 experiments each, preferential formation of both enantiomers of the newly formed product was observed: seven times S and three times R in the case of 1a and six times S and four times R in the case of 1b.

Oxidation of Ammonia Catalyzed by a Molecular Iron Complex: Translating Chemical Catalysis to Mediated Electrocatalysis

Ammonia is a promising candidate in the quest for sustainable, clean energy. With its capacity to serve as an energy carrier, the oxidation of ammonia opens avenues for carbon-neutral approaches to address worldwide growing energy needs. We report the catalytic chemical oxidation of ammonia by an Earth-abundant transition metal complex, trans-[LFeII(MeCN)2][PF6]2, where L is a macrocyclic ligand bearing four N-heterocyclic carbene (NHC) donors. Using triarylaminium radical cations in MeCN, up to 182 turnovers of N2 per Fe were obtained from chemical catalysis with an extremely low loading of the Fe catalyst (0.043 mM, 0.004 mol % catalyst). This chemical catalysis was successfully transitioned to mediated electrocatalysis for the oxidation of ammonia. Molecular electrocatalysis by the Fe catalyst and the mediator (p-MeOC6H4)3N exhibited a catalytic half-wave potential (Ecat/2) of 0.18 V vs [Cp2Fe]+/0 in MeCN, and achieved 9.3 turnovers of N2 at an applied potential of 0.20 V vs [Cp2Fe]+/0 at -20 °C in controlled-potential electrolysis, with a Faradaic efficiency of 75 %. Based on computational results, the catalyst undergoes sequential oxidation and deprotonation steps to form [LFeIV(NH2)2]2+, and thereafter bimetallic coupling to form an N-N bond.

A decarbonylative approach to alkylnickel intermediates and C(sp3)-C(sp3) bond formation

The myriad nickel-catalyzed cross-coupling reactions rely on the formation of an organonickel intermediate, but limitations in forming monoalkylnickel species have limited options for C(sp3) cross-coupling. The formation of monoalkylnickel(II) species from abundant carboxylic acid esters would be valuable, but carboxylic acid derivatives are primarily decarboxylated to form alkyl radicals that lack the correct reactivity. In this work, we disclose a facile oxidative addition and decarbonylation sequence that forms monoalkylnickel(II) intermediates through a nonradical process. The key ligand, bis(4-methylpyrazole)pyridine, accelerates decarbonylation, stabilizes the alkylnickel(II) intermediate, and destabilizes off-cycle nickel(0) carbonyl species. The utility of this new reactivity in C(sp3)-C(sp3) bond formation is demonstrated in a reaction that is challenging by purely radical methods-the selective cross-coupling of primary carboxylic acid esters with primary alkyl iodides.

Mechanistic Insight of High-Valent First-Row Transition Metal Complexes for Dehydrogenation of Ammonia Borane

Designing an efficient and cost-effective catalyst for ammonia borane (AB) dehydrogenation remains a persistent challenge in advancing a hydrogen-based economy. Transition metal complexes, known for their C-H bond activation capabilities, have emerged as promising candidates for AB dehydrogenation. In this study, we investigated two recently synthesized C-H activation catalysts, 1 (CoIV-dinitrate complex) and 2 (NiIV-nitrate complex), and demonstrated their efficacy for AB dehydrogenation. Using density functional theory calculations and a detailed analysis, we elucidated the AB dehydrogenation mechanism of these complexes. Our results revealed that both complexes 1 and 2 can efficiently dehydrogenate AB at room temperature, although the abstraction of molecular H2 from these complexes requires slightly elevated temperatures. We utilized H2 binding free energy calculations to identify potentially active sites and observed that complex 2 can release two equivalents of H2 at a temperature slightly higher than room temperature. Furthermore, we investigated AB dehydrogenation kinetics and thermodynamics in iron (Fe)-substituted systems, complexes 3 and 4. Our results showed that the strategic alteration of the central metal atom, replacing Ni in complex 2 with Fe in complex 4, resulted in enhanced kinetics and thermodynamics for AB dehydrogenation in the initial cycle. These results underscore the potential of high-valent first-row transition metal complexes for facilitating AB dehydrogenation at room temperature. Additionally, our study highlights the beneficial impact of incorporating iron into such mononuclear systems, enhancing their catalytic activity.

Probing the Electric Field Response of a Water Molecule Confined in Small Carbon Nanocages: A Density Functional Theory Investigation

We consider a water molecule under tight confinement in the small-sized fullerenes (C28 ${_{28} }$ , C30 ${_{30} }$ , C32 ${_{32} }$ ) within the density functional theory (DFT) calculations with suitable exchange-correlation functionals. Such nanoscopic molecular cages provide an ideal setup to study their characteristic properties not present in the condensed phase. The water molecule entirely loses its feature of typical water when it is confined in small fullerenes of size equal to C30 ${_{30} }$ or smaller, in which the asymmetric O-H stretching vibration occurs at a lower wavenumber than the symmetric stretching. We study the response of the confined water molecule to the applied electric fields in terms of change in geometrical parameters, NMR spin-spin coupling constants, dipole moment, HOMO-LUMO (HL) gap, and vibrational frequency shift. The electric field shielding property of small-sized fullerene cages is explored and found to be strongly correlated with the HL gap. Since the electric field modulates the gap to decrease generally, shielding efficiency varies with field strength, thereby making large fields better shielded than small fields for the small penetration factor at large fields. The results that hold significance for technological applications are discussed.

Theoretical Investigation on the Reversible Photoswitch Mechanism of Benzylidene-Oxazolone System

The design and application of molecular photoswitches have attracted much attention. Herein, we performed a detailed computational study on the photoswitch benzylidene-oxazolone system based on static electronic structure calculations and on-the-fly excited-state dynamic simulations. For the Z and E isomer, we located six and four minimum energy conical intersections (MECIs) between the first excited state (S1) and the ground state (S0), respectively. Among them, the relaxation pathway driven by ring-puckering motion is the most competitive channel with the photoisomeization process, leading to the low photoisomerization quantum yield. In the dynamic simulations, about 88 % and 66 % trajectories decay from S1 to S0 for Z and E isomer, respectively, within the total simulation time of ~2 ps. The photoisomeization quantum yields obtained in our study (0.20 for Z→E and 0.12 for E→Z) agree well with the experimental measured values (0.25 and 0.11), even though the number of trajectories is limited to 50. Our study sheds light on the complexity of the benzylidene-oxazolone system 's deactivation process and the competitive mechanisms among different reaction channels, which provides theoretical guidance for further design and development of benzylidene-oxazolone based molecular photoswitches.

Microglial Neuroinflammation-Independent Reversal of Demyelination of Corpus Callosum by Arsenic in a Cuprizone-Induced Demyelinating Mouse Model

Demyelination is the loss of myelin in CNS, resulting in damaged myelin sheath. Oxidative stress and neuroinflammation play a key role in inducing demyelinating diseases like MS; hence, controlling oxidative stress and neuroinflammation is important. Cuprizone (CPZ), a copper chelator, generates oxidative stress and neuroinflammation, thereby inducing demyelination. Therefore, the CPZ-induced demyelinating mouse model (CPZ model) is widely used in research. The present study was intended to unravel a mechanism of inhibition of demyelination by arsenic in a CPZ model, which is otherwise known for its toxicity. We investigated an alternative mechanism of inhibition of demyelination by arsenic through the reversal of SOD1 activity employing in silico analysis, analytical chemistry techniques, and in vitro and in vivo experiments. In vivo experiments showed protection of body weight, survivability, and myelination of the corpus callosum in CPZ and arsenic-co-exposed animals, where neuroinflammation was apparently not involved. In vitro experiments revealed that arsenic-mediated reversal of impaired SOD1 activity leads to reduced cellular ROS levels and better viability of primary oligodendrocytes. Reversal of SOD1 activity was also observed in the corpus callosum tissue isolated from experimental animals. In silico and analytical chemistry studies revealed that similar to copper, arsenic can potentially bind to CPZ and thereby make the copper freely available for SOD1 activity. Suitable neurobehavior tests further validated the protective effect of arsenic. Taken together, the present study revealed that arsenic protects oligodendrocytes and demyelination of corpus callosum by reversing CPZ-induced impaired SOD1 activity.

Eosin Y Catalyzed Photochemical Synthesis of Arylated Phenothiazones

In the presence of Eosin Y (EY), the synthesis of substituted phenothiazones was carried out efficiently using various substituted 2-aminothiophenol, diazonium salts, and 1,4-napthaquinones (1,4-NQ) at room temperature (RT) (condition: green LED of 525 nm, 44 W; reaction time: 8 h, isolated yield: 68-90%). A fluorescence quenching experiment and density functional theory (DFT) calculations suggested that the triplet photoexcited state of EY (EY*; τT = 320 ± 10 ns) converts to EY+• via oxidative quenching by ArN2 + (-1.11 V vs SCE for EY* to EY+•) initially. Thiyl and aryl radicals were captured as TEMPO adducts in high-resolution mass spectroscopy (HRMS). The reaction was not inhibited by the addition of a singlet oxygen quencher such as 1,4-diazobicyclo [2.2.2] octane (DABCO), which suggests that singlet oxygen is not participated.

Spectroscopic Manifestations of (Anti)Aromaticity in Oxidized and Reduced Porphyrin and Norcorrole

Aromaticity and antiaromaticity are foundational principes in organic chemistry, regularly invoked to explain stability, structure, and magnetic and electronic properties. There are ongoing challenges in assigning molecules as aromatic or antiaromatic using optical spectroscopy. Here we report spectroelectrochemical and computational analyses of porphyrin (18π neutral, aromatic) and norcorrole (16π neutral, antiaromatic), and their oxidized (16π porphyrin dication) and reduced (norcorrole 18π dianion) forms. Our results show that while the visible spectra are characteristic of (anti)aromaticity consistent with Hückel's rules, the IR spectra are much less informative, owing to the relative rigidity of norcorrole. The results have implications for the assignment of (anti)aromaticity in both ground-state and time-resolved spectra.

Postsynthetically Modified Cationic, Robust MOF Featuring Selective Separation of Carboxylate-Containing Pharmaceutical Drugs from Water at Neutral pH: Elucidation of the Adsorption Mechanism by Theory and Experiments

The escalating levels of hazardous pharmaceutical contaminants, specifically nonsteroidal anti-inflammatory drugs (NSAIDs), in groundwater reservoir surfaces and surface waterway systems have prompted substantial scientific interest regarding their potential deleterious effects on both aquatic ecosystems and human health. Extraction of those pollutants from wastewater is quite challenging. Hence, the development of economic, sustainable, and scalable techniques for capturing and removing those pollutants is crucial to ensure water safety. Herein, we demonstrate a physicochemically stable, reusable, porous Hf(IV)-based cationic metal-organic framework (MOF), namely, 1'@MeCl for the aqueous phase adsorption-based removal of NSAIDs (diclofenac, naproxen, ibuprofen) from the wastewater environment. The highly positively charged surface of the 1'@MeCl MOF enables it to selectively extract more than 99% of diclofenac, naproxen, and ibuprofen contaminants within less than 30 s. With fast adsorption kinetics, very high adsorption capacities (Qe) were achieved at neutral pH for diclofenac (482.9 mg/g), naproxen (295.9 mg/g), and ibuprofen (219.5 mg/g). Moreover, the influence of changes in pH and coexisting anions on the adsorption property of the 1'@MeCl MOF was studied. Furthermore, the adsorption efficiency of 1'@MeCl in different real water environments was ensured by performing diclofenac, naproxen, and ibuprofen adsorption from tap, river, and lake water. Moreover, a 1'@MeCl-anchored cellulose acetate-chitosan membrane was developed successfully to demonstrate the membrane-based extraction of diclofenac, naproxen, and ibuprofen from contaminated water. Furthermore, a molecular-level mechanistic study was performed through experimental and computational study to propose the plausible adsorption mechanisms for diclofenac, naproxen, and ibuprofen over the surface of 1'@MeCl.

Trans-Concerted Addition to Alkynes: the case of Ynamide Silylzincation

An original concerted antarafacial mechanism for the addition of diorganosilyl-zinc reagents across the C-C triple bond of ynamides is computationally investigated using DFT calculations. This concerted mechanism, leading to a trans-product in only one step, results in the formation of a Si-C and a Zn-C σ-bond on opposite sides of the π-system. We demonstrate that the mechanism going through a η2-vinyl intermediate and the proposal of a radical chain pathway are energetically unsustainable. The retained concerted antarafacial pathway is tested on experimental selectivities: the regioselectivity, in favor of the silyl β-addition in ynamide, and stereoselectivity, which is cis- with (Me2PhSi)2Zn but trans- with [(Me3Si)3Si]2Zn, are well reproduced by DFT calculations. The regio- and stereoselectivity are discussed using the activation strain model and a chemical bonding analysis.

A family of Cd(II) coordination polymers constructed from 6-aminopicolinate and bipyridyl co-linkers: study of their growth in paper and photoluminescence sensing of Fe3+ and Zn2+ ions

In this work, we report on five novel coordination polymers (CPs) based on the linkage of the [Cd(6apic)2] building block [where 6apic = 6-aminopicolinate] by different bipyridine-type organic spacers, forming different coordination compounds with the following formulae: [Cd(μ-6apic)2]n (1), {[Cd(6apic)2(μ-bipy)]·H2O}n (2), {[Cd(6apic)2(μ-bpe)]·2H2O}n (3), [Cd(6apic)(μ-6apic)(μ-bpa)0.5]n (4) and {[Cd2(6apic)4(μ-tmbp)]·7H2O}n (5) [where bipy = 4,4'-bipyridine, bpe = 1,2-di(4-pyridyl)ethylene, bpa = 1,2-di(4-pyridyl)ethane (bpa) and tmbp = 1,3-di(4-pyridyl)propane]. Most of the synthesized compounds form infinite metal-organic rods through the linkage of the building block by the bipyridine-type linker, except in the case of compound 4 whose assembly forms a densely packed 3D architecture. All compounds were fully characterized and their photoluminescence properties were studied experimentally and computationally through density functional theory (DFT) calculations. All compounds display, upon UV excitation, a similar blue emission of variable intensity depending on the linker employed for the connection of the building units, among which compound 2 deserves to be highlighted for its room temperature phosphorescence (RTP) with an emission lifetime of 32 ms that extends to 79 ms at low temperature. These good photoluminescence properties, in addition to its stability in water over a wide pH range (between 2 and 10), motivated us to study compound 2 as a sensor for the detection of metal ions in water, and it showed high sensitivity to Fe3+ through a fluorescence turn-off mechanism and an unspecific turn-on response to Zn2+. Furthermore, the compound is processed as a paper-based analytical device (PAD) in which the phosphorescence emission is preserved, improving the sensing capacity toward Fe3+ ions.

Efficiency and Mechanism of Catalytic Siloxane Exchange in Vitrimer Polymers: Modeling and Density Functional Theory Investigations

Of late, siloxane-containing vitrimers have gained significant interest due to their fast dynamic characteristics over a reasonable temperature range (180-220 °C), making them well-suited for diverse applications. The exchange reaction pathway in the siloxane vitrimers is accountable for the covalent adaptive network, with the reaction's effectiveness being regulated by either organic or organometallic catalysts. However, directly studying the exchange reaction pathway in the bulk phase using experimental approaches is challenging because of the intricate and interconnected structure of these vitrimers. Here, we perform comprehensive density functional theory (DFT) and experimental investigations to discover the detailed catalytic efficacy of siloxane exchange and provide direction for the reaction process using a 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) catalyst. The calculated transition barrier energy and catalytic efficiency of hexamethyldisiloxane and dihydroxy-dimethylsilane exchange derived from the nudged elastic band with transition-state calculations strongly agree with the experimental findings. In addition, Fukui indices, along with partial charges, are employed to evaluate the nucleophilic and electrophilic behaviors of silanol and siloxane molecules. Our analysis revealed that by utilizing the Fukui indices of both the acid and the base, we can make an approximate estimation of the respective kinetics of the SN2 process in the siloxane exchange reaction mechanism. These findings establish a foundation for comprehending a crucial aspect of the exchange mechanism in siloxane vitrimer systems and could aid in the development of novel catalysts.

Cerium(III) and 5-methylisophthalate-based MOFs with slow relaxation of magnetization and photoluminescence emission

Two novel Ce(III) metal organic frameworks (MOFs) with formulas [Ce(5Meip)(H-5Meip)]nGR-MOF-17 and [CeCl(5Meip)(DMF)]nGR-MOF-18 (5Meip = 5-methylisophthalate, DMF = N,N-dimethylformamide) have been synthesized, forming 3-dimensional frameworks. Magnetic measurements show that both compounds present field-induced slow magnetic relaxation under a small applied dc field. For GR-MOF-17, the temperature dependence of relaxation times is best described by a Raman mechanism, whereas for GR-MOF-18, relaxation occurs through a combination of Raman and local-mode pathways. Moreover, when avoiding short Ce⋯Ce interactions by magnetic dilution in GR-MOF-17@La and GR-MOF-18@La, only the local-mode mechanism is responsible for magnetic relaxation. Photophysical studies show the occurrence of ligand-centred luminescence in both compounds and phosphorescence emission at low temperature for GR-MOF-17.

Different Effects of Strong-Bonded Water with Different Degrees of Substitution of Sodium Sulfobutylether-β-cyclodextrin on Encapsulation

The encapsulation of sodium sulfobutylether-β-cyclodextrin (SBE-β-CD) is influenced not only by the degree of substitution (DS) but also by the presence of strong-bonded water (SBW). Guests compete with SBW for positions within the cavity of SBE-β-CD. However, the correlation between DS and SBW was not clear. This study revealed a positive correlation between DS and SBW utilizing Karl Fischer titration. The mechanism may be attributed to molecular polarizability. To explore the impact of SBW inside SBE-β-CD with different DS on encapsulation, density functional theory was employed. Throughout the release process, an increase in enthalpy is unfavorable, while an increase in entropy favors spontaneous reaction occurrence. For SBE-β-CD (DS = 2, 3), enthalpy increase is the primary factor, leading to the retention of SBW within the cavities and consequently hindering guest entry. In contrast, for SBE-β-CD (DS = 4, 7), the situation differs. For SBE10-β-CD, the influence of SBW is minimal. This study aims to elucidate the relationship between DS and SBW, as well as the effect of SBW inside SBE-β-CD with different DS on encapsulation. It is crucial for a comprehensive understanding of the factors affecting the encapsulation of SBE-β-CD, thereby promoting quality control and functional development of SBE-β-CD.

A Co(III)-peroxo-arylboronate complex formed by nucleophilic reaction of a Co(III)-peroxo species

In this work, we report the generation and characterization of two new Co(III)-peroxo complexes 2 and 3. 2 is best described as a mononuclear CoIII-(O2) complex that exhibits an 18O-isotope sensitive OO bond stretching vibration at 845(-49) cm-1, indicating a relatively weak peroxo moiety compared to those of other CoIII-(O2) complexes reported previously. Complex 3 is a CoIII-peroxo-arylboronate species having a rare {CoIIIOOBO} five-membered metallocycle, which is structurally characterized using X-ray crystallography. Investigations of the reaction mechanism using density functional theory calculations show that 2 likely undergoes a nucleophilic attack to an arylboronic acid, which is generated by hydrolysis of the BPh4- anion in wet acetonitrile solution, to first form a CoIII-peroxo-arylboronic acid adduct, followed by the loss of one benzene molecule to generate the five-membered metallocycle. The entire reaction is thermodynamically favorable. Taken together, the conversion of 2 to 3 represents the discovery of a novel nucleophilic reactivity that can be carried out by mononuclear Co(III)-peroxo complexes.

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.

Multifunctional Organometallic Compounds Active against Infective Trypanosomes: Ru(II) Ferrocenyl Derivatives with Two Different Bioactive Ligands

Human African trypanosomiasis (HAT, sleeping sickness) and American trypanosomiasis (Chagas disease) are endemic zoonotic diseases caused by genomically related trypanosomatid protozoan parasites (Trypanosoma brucei and Trypanosoma cruzi, respectively). Just a few old drugs are available for their treatment, with most of them sharing poor safety, efficacy, and pharmacokinetic profiles. Only fexinidazole has been recently incorporated into the arsenal for the treatment of HAT. In this work, new multifunctional Ru(II) ferrocenyl compounds were rationally designed as potential agents against these pathogens by including in a single molecule 1,1'-bis(diphenylphosphino)ferrocene (dppf) and two bioactive bidentate ligands: pyridine-2-thiolato-1-oxide ligand (mpo) and polypyridyl ligands (NN). Three [Ru(mpo)(dppf)(NN)](PF6) compounds and their derivatives with chloride as a counterion were synthesized and fully characterized in solid state and solution. They showed in vitro activity on bloodstream T. brucei (EC50 = 31-160 nM) and on T. cruzi trypomastigotes (EC50 = 190-410 nM). Compounds showed the lowest EC50 values on T. brucei when compared to the whole set of metal-based compounds previously developed by us. In addition, several of the Ru compounds showed good selectivity toward the parasites, particularly against the highly proliferative bloodstream form of T. brucei. Interaction with DNA and generation of reactive oxygen species (ROS) were ruled out as potential targets and modes of action of the Ru compounds. Biochemical assays and in silico analysis led to the insight that they are able to inhibit the NADH-dependent fumarate reductase from T. cruzi. One representative hit induced a mild oxidation of low molecular weight thiols in T. brucei. The compounds were stable for at least 72 h in two different media and more lipophilic than both bioactive ligands, mpo and NN. An initial assessment of the therapeutic efficacy of one of the most potent and selective candidates, [Ru(mpo)(dppf)(bipy)]Cl, was performed using a murine infection model of acute African trypanosomiasis. This hit compound lacks acute toxicity when applied to animals in the dose/regimen described, but was unable to control parasite proliferation in vivo, probably because of its rapid clearance or low biodistribution in the extracellular fluids. Future studies should investigate the pharmacokinetics of this compound in vivo and involve further research to gain deeper insight into the mechanism of action of the compounds.

Quantum Chemical Investigation into the Structural Analysis and Calculated Raman Spectra of Amylose Modeled with Linked Glucose Molecules

This study presents a quantum chemical investigation into the structural analysis and calculated Raman spectra of modeled amylose with varying units of linked glucose molecules. We systematically examined the rotation of hydroxymethyl groups and intramolecular hydrogen bonds within these amylose models. Our study found that as the number of linked glucose units increases, the linear structure becomes more complex, resulting in curled, cyclic, or helical structures facilitated by establishing various intramolecular interactions. The hydroxymethyl groups were confirmed to form interactions with oxygen atoms and with hydroxymethyl and hydroxyl groups from adjacent rings in the molecular structures. We identified distinct peaks and selected specific bands applicable in various analytical contexts by comparing their calculated Raman spectra. Representative vibrational modes within selected regions were identified across the different lengths of amylose models, serving as characteristic signatures for linear and more coiled structural conformations. Our findings contribute to a deeper understanding of amylose structures and spectroscopic signatures, with implications for theoretical studies and potential applications. This work provides valuable reference points for the detailed assignment of Raman peaks of amylose structure, facilitating their application in broader research on carbohydrate structures and their associated spectroscopic properties.

Molecular modeling of multi-target analogs of huperzine A and applications in Alzheimer's disease

CONTEXT

Given the diverse pathophysiological mechanisms underlying Alzheimer's disease, it is improbable that a single targeted drug will prove successful as a therapeutic strategy. Therefore, exploring various hypotheses in drug design is imperative. The sequestration of Fe(II) and Zn(II) cations stands out as a crucial mechanism based on the mitigation of reactive oxygen species. Moreover, inhibiting acetylcholinesterase represents a pivotal strategy to enhance acetylcholine levels in the synaptic cleft. This research aims to investigate the analogs of Huperzine A, documented in scientific literature, considering of these two hypotheses. Consequently, the speciation chemistry of these structures with Fe(II) and Zn(II) was scrutinized using quantum chemistry calculations, molecular docking simulations, and theoretical predictions of pharmacokinetics properties. From the pharmacokinetic properties, only two analogs, HupA-A1 and HupA-A2, exhibited a theoretical permeability across the blood-brain barrier; on the other hand, from a thermodynamic standpoint, the enantiomers of HupA-A2 showed negligible chelation values. The enantiomers with the most favorable interaction parameters were S'R'HupA-A1 (ΔGBIND = -40.0 kcal mol-1, fitness score = 35.5) and R'R'HupA-A1 (ΔGBIND = -35.5 kcal mol-1, fitness score = 22.61), being compared with HupA (ΔGBIND = -41.75 kcal mol-1, fitness score = 39.95). From this study, some prime candidates for promising drug were S'R'HupA-A1 and R'R'HupA-A1, primarily owing to their favorable thermodynamic chelating capability and potential anticholinesterase mechanism.

METHODS

Quantum chemistry calculations were carried out at B3LYP/6-31G(d) level, considering the IEF-PCM(UFF) implicit solvent model for water. The coordination compounds were assessed using the Gibbs free energy variation and hard and soft acid theory. Molecular docking calculations were conducted using the GOLD program, based on the crystal structure of the acetylcholinesterase protein (PDB code = 4EY5), where the ChemScore function was employed with the active site defined as the region within a 15-Å radius around the centroid coordinates (X = -9.557583, Y = -43.910473, Z = 31.466687). Pharmacokinetic properties were predicted using SwissADME, focusing on Lipinski's rule of five.

Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators

Long-range electrostatic effects are fundamental for describing chemical reactivity in the condensed phase. Here, we present the methodology of an efficient quantum mechanical/molecular mechanical (QM/MM) model in periodic boundary conditions (PBC) compatible with QM/MM boundaries at chemical bonds. The method combines electrostatic potential fitted charge operators and electrostatic potentials derived from the smooth particle-mesh Ewald (PME) sum approach. The total energy and its analytic first derivatives with respect to QM, MM, and lattice vectors allow QM/MM molecular dynamics (MD) in the most common thermodynamic ensembles. We demonstrate the robustness of the method by performing a QM/MM MD equilibration of methanol in water. We simulate the cis/trans isomerization free-energy profiles in water of proline amino acid and a proline-containing oligopeptide, showing a correct description of the reaction barrier. Our PBC-compatible QM/MM model can efficiently be used to study the chemical reactivity in the condensed phase and enzymatic catalysis.

Conformational and environmental effects on the electronic and vibrational properties of dyes for solar cell devices

The main challenge for solar cell devices is harvesting photons beyond the visible by reaching the red-edge (650-780 nm). Dye-sensitized solar cell (DSSC) devices combine the optical absorption and the charge separation processes by the association of a sensitizer as a light-absorbing material (dye molecules, whose absorption can be tuned and designed) with a wide band gap nanostructured semiconductor. Conformational and environmental effects (i.e., solvent, pH) can drastically influence the photophysical properties of molecular dyes. This study proposes a combined experimental and computational approach for the comprehensive investigation of the electronic and vibrational properties of a unique class of organic dye compounds belonging to the family of red-absorbing dyes, known as squaraines. Our focus lies on elucidating the intricate interplay between the molecular structure, vibrational dynamics, and optical properties of squaraines using state-of-the-art density functional theory calculations and spectroscopic techniques. Through systematic vibrational and optical analyses, we show that (i) the main absorption peak in the visible range is influenced by the conformational and protonation equilibria, (ii) the solvent polarity tunes the position of the UV-vis absorption, and (iii) the vibrational spectroscopy techniques (infrared and Raman) can be used as informative tools to distinguish between different conformations and protonation states. This comprehensive understanding offers valuable insights into the design and optimization of squaraine-based DSSCs for enhanced solar energy conversion efficiency.

Urethane Synthesis in the Presence of Organic Acid Catalysts-A Computational Study

A general mechanism for catalytic urethane formation in the presence of acid catalysts, dimethyl hydrogen phosphate (DMHP), methanesulfonic acid (MSA), and trifluoromethanesulfonic acid (TFMSA), has been studied using theoretical methods. The reaction of phenyl isocyanate (PhNCO) and butan-1-ol (BuOH) has been selected to describe the energetic and structural features of the catalyst-free urethane formation. The catalytic activities of DMHP, MSA, and TFMSA have been compared by adding them to the PhNCO-BuOH model system. The thermodynamic properties of the reactions were computed by using the G3MP2BHandHLYP composite method. It was revealed that in the presence of trifluoromethanesulfonic acid, the activation energy was the lowest within the studied set of catalysts. The achieved results indicate that acids can be successfully employed in urethane synthesis and the mechanism was described.

Unique solvation structure induced by anionic Cl in aqueous zinc ion batteries

Aqueous zinc ion batteries (AZIBs) have garnered significant attention in large-scale static energy storage battery systems due to their low cost, high safety and environmental friendliness. However, it has some inherent problems during operation, such as the occurrence of side reactions (hydrogen evolution reaction, HER) and anode corrosion, formation of by-products and growth of metal dendrites. To analyze the mechanism of generation from aspect of the electrolyte solvation structure and make cell efficiency further improvements based on it, so we use DFT calculations to find the most stable solvation structure in AZIBs with ZnCl2 as the electrolyte and analyze it. We define the relative concentration C r , and calculate different groups metal cation cluster structures such as [ Zn ( H 2 O ) n ] 2 + , [ ZnCl ( H 2 O ) n ] + , [ ZnCl 2 ( H 2 O ) n ] and [ ZnCl 3 ( H 2 O ) n ] - that exist at different C r . We discuss the effect of different clusters formed due to the C r variations on the battery performance in terms of three aspects: the structural conformation, the cluster characteristics (including the hydrogen bonding network, bond lengths, bond angles, as well as the electrostatic potential ESP) and the cluster performance (including the adsorption energy Ea, binding energy Eb, and desolvation energy Edes). The results shows that the electrolyte metal cation Zn2+ can be coordinated with up to six H2O molecules in first shell, and this metal cation solvation structure contributes to the occurrence and formation of side reactions and by-products, which reduces the battery efficiency. Increasing the electrolyte anion Cl- concentration by appropriately increasing the C r helps to desolvate the metal cation cluster structure, which greatly improves the battery efficiency and suppresses the side reactions and by-products. Yet the improvement effect was not obviously further improved by further increasing the Cl- concentration.

An Electronic Structure Investigation of PEDOT with AlCl4- Anions-A Promising Redox Combination for Energy Storage Applications

In this work, we use density functional theory to investigate the electronic structure of poly(3,4-ethylenedioxythiophene) (PEDOT) oligomers with co-located AlCl4- anions, a promising combination for energy storage. The 1980s bipolaron model remains the dominant interpretation of the electronic structure of PEDOT despite recent theoretical progress that has provided new definitions of bipolarons and polarons. By considering the influence of oligomer length, oxidation or anion concentration and spin state, we find no evidence for many of the assertions of the 1980s bipolaron model and so further contribute to a new understanding. No self-localisation of positive charges in PEDOT is found, as predicted by the bipolaron model at the hybrid functional level. Instead, our results show distortions that exhibit a single or a double peak in bond length alternations and charge density. Either can occur at different oxidation or anion concentrations. Rather than representing bipolarons or polaron pairs in the original model, these are electron distributions driven by a range of factors. Distortions can span an arbitrary number of nearby anions. We also contribute a novel conductivity hypothesis. Conductivity in conducting polymers has been observed to reduce at anion concentrations above 0.5. We show that at high anion concentrations, the energy of the localised, non-bonding anionic orbitals approaches that of the system HOMO due to Coulombic repulsion between anions. We hypothesize that with nucleic motion in the macropolymer, these orbitals will interfere with the hopping of charge carriers between sites of similar energy, lowering conductivity.

Argentophilic Interactions, Flexibility, and Dynamics of Pyrrole Cages Encapsulating Silver(I) Clusters

Recently, pyrrole cages have been synthesized that encapsulate ion pairs and silver(I) clusters to form intricate supramolecular capsules. We report here a computational analysis of these structures using density functional theory combined with a semiempirical tight-binding approach. We find that for neutral pyrrole cages, the Gibbs free energies of formation provide reliable predictions for the ratio of bound ions. For charged pyrrole cages, we find strong argentophilic interactions between Ag ions on the basis of the calculated bond indices and molecular orbitals. For the cage with the Ag4 cluster, we find two minimum-geometry conformations that differ by only 6.5 kcal/mol, with an energy barrier <1 kcal/mol, suggesting a very flexible structure as indicated by molecular dynamics. The predicted energies of formation of [Agn⊂1]n-3+ (n = 1-5) cryptands provide low energy barriers of formation of 5-20 kcal/mol for all cases, which is consistent with the experimental data. Furthermore, we also examined the structural variability of mixed-valence silver clusters to test whether additional geometrical conformations inside the organic cage are thermodynamically accessible. In this context, we show that the time-dependent density functional theory UV-vis spectra may potentially serve as a diagnostic probe to characterize mixed-valence and geometrical configurations of silver clusters encapsulated into cryptands.

Excited-state dynamics of 4-hydroxyisoindoline-1,3-dione and its derivative as fluorescent probes

Fluorescent probes have become promising tools for monitoring the concentration of peroxynitrite, which is linked to many diseases. However, despite focusing on developing numerous peroxynitrite based fluorescent probes, limited emphasis is placed on their sensing mechanism. Here, we investigated the sensing mechanism of a peroxynitrite fluorescent probe, named BHID-Bpin, with a focus on the relevant excited state dynamics. The photoexcited BHID-Bpin relaxes to its ground state via an efficient nonradiative process (∼300 ps) due to the presence of a minimum energy conical intersection between its first excited state and ground state. However, upon reacting with peroxynitrite, the Bpin moiety is cleaved from BHID-Bpin and BHID is formed. The formed BHID exhibits strong dual band fluorescence which is caused by an ultrafast excited-state intramolecular proton transfer process (∼1 ps).

Unravelling the role of spin-vibrational coupling in designing high-performance pentagonal bipyramidal Dy(iii) single ion magnets

At the cutting edge of high-performance single-molecule magnets (SMMs) lie lanthanide-based complexes, renowned for their potent magnetic anisotropy. SMMs containing one metal centre are defined as single-ion magnets (SIMs). The performance of SMMs is measured generally via the barrier height for magnetisation reversal (Ueff) and blocking temperature (TB), below which the magnetisation is fully frozen. To enhance the Ueff and TB values in lanthanide-based SMMs, the static crystal field splitting of mJ levels has been effectively adjusted through ligand design, leveraging the oblate/prolate ground state 4f electron density shape. However, the maximum fine-tuning achievable through ligand design, known as the axial limit, has already been reached in this class of compounds. This necessitates new design principles to enhance SMM characteristics to better suit end-user applications. Among other avenues that can be explored to improve SMM characteristics, a deeper understanding of spin-phonon coupling is critical to advancing TB values. However, there are only a handful of examples where this has been deciphered. In this work, using a combination of DFT and ab initio CASSCF calculations, we have performed spin-phonon calculations on five classes of pentagonal bipyramidal Dy(iii) SIMs exhibiting TB values in the range of 4.5 K to 36 K ([Dy(bbpen)Br] (1, H2bbpen = N,N'-bis(2-hydroxybenzyl)-N,N'-bis(2-methylpyridyl)ethylenediamine), [Dy(OCMe3)Br(THF)5][BPh4] (2) [Dy(OSiMe3)Br(THF)5] [BPh4] (3), [Dy(LN5)(Ph3SiO)2](BPh4)·CH2Cl2 (4) and [L2Dy(H2O)5][I]3·L2·H2O (5, L = tBuPO(NHiPr)2)). Unlike the method employed elsewhere for the calculation of spin-phonon coupling, in this work, we have employed a set of criteria and intuitively selected vibrational modes to perform the spin-phonon coupling analysis. The approach provided here not only reduces the computational cost significantly but also suggests chemical intuition to improve the performance of this class of compounds. Our calculations reveal that low-energy vibrational modes govern the magnetisation relaxation in these SIMs. A flexible first coordination sphere found on some of the complexes was found to be responsible for low-energy vibrations that flip the magnetisation, reducing the TB values drastically (complexes 2 and 3). On the other hand, a rigid first coordination sphere and a stiff ligand framework move the spin-vibrational coupling that causes the relaxation to lie beyond the secondary coordination sphere, resulting in an increase in TB values. Our calculations also reveal that not only the atoms in the first coordination sphere but also those in the secondary coordination sphere affect the performance of the SMMs. Learning from this exercise, we have undertaken several in silico models based on these vibrations to improve the TB values. Some of these predictions were correlated with literature precedents, offering confidence in the methodology employed. To this end, our comprehensive investigation, involving twenty-three molecules/models and five sets of geometries for pentagonal bipyramidal Dy(iii) single-ion magnets (SIMs), unveils a treasure trove of chemically sound design clues, poised to enhance the TB values in this fascinating molecular realm.

Reactivity of Superbasic Carbanions Generated via Reductive Radical-Polar Crossover in the Context of Photoredox Catalysis

Photocatalytic reactions involving a reductive radical-polar crossover (RRPCO) generate intermediates with carbanionic reactivity. Many of these proposed intermediates resemble highly reactive organometallic compounds. However, conditions of their formation are generally not tolerated by their isolated organometallic versions and often a different reactivity is observed. Our investigations on their nature and reactivity under commonly used photocatalytic conditions demonstrate that these intermediates are indeed best described as free, superbasic carbanions capable of deprotonating common polar solvents usually assumed to be inert such as acetonitrile, dimethylformamide, and dimethylsulfoxide. Their basicity not only towards solvents but also towards electrophiles, such as aldehydes, ketones, and esters, is comparable to the reactivity of isolated carbanions in the gas-phase. Previously unsuccessful transformations thought to result from a lack of reactivity are explained by their high reactivity towards the solvent and weakly acidic protons of reaction partners. An intuitive explanation for the mode of action of photocatalytically generated carbanions is provided, which enables methods to verify reaction mechanisms proposed to involve an RRPCO step and to identify the reasons for the limitations of current methods.

Fingerprint of Dipole Moment Orientation of Water Molecules in Cu2+ Aqueous Solution Probed by X-ray Photoelectron Spectroscopy

The electronic structure and geometrical organization of aqueous Cu2+ have been investigated by using X-ray photoelectron spectroscopy (XPS) at the Cu L-edge combined with state-of-the-art ab initio molecular dynamics and a quantum molecular approach designed to simulate the Cu 2p X-ray photoelectron spectrum. The calculations offer a comprehensive insight into the origin of the main peak and satellite features. It is illustrated how the energy drop of the Cu 3d levels (≈7 eV) following the creation of the Cu 2p core hole switches the nature of the highest singly occupied molecular orbitals (MOs) from the dominant metal to the dominant MO nature of water. It is particularly revealed how the repositioning of the Cu 3d levels induces the formation of new bonding (B) and antibonding (AB) orbitals, from which shakeup mechanisms toward the relaxed H-SOMO operate. As highlighted in this study, the appearance of the shoulder near the main peak corresponds to the characteristic signature of shakeup intraligand (1a1 → H-SOMO(1b1)) excitations in water, providing insights into the average dipole moment distribution (≈36°) of the first-shell water molecules surrounding the metal ion and its direct impact on the broadening of the satellite. It is also revealed that the main satellite at 8 eV from the main peak corresponds to (metal/1b2 → H-SOMO(1b1) of water) excitations due to a bonding/antibonding (B/AB) interaction of Cu 3d levels with the deepest valence O2p/H1s 1b2 orbitals of water. This finding underscores the sensitivity of XPS to the electronic structure and orientation of the nearest water molecules around the central ion.

Density Functional Theory Calculation May Confirm Arsenic-Thiol Adhesion as the Primary Mechanism of Arsenical Toxicity

Previously, it was believed that methylation was the body's primary method to detoxify inorganic arsenic. However, recent research has shown that the metabolized intermediate known as MMAIII is more toxic than arsenite and arsenate, contradicting a previous understanding. Another important question arises: is arsenical toxicity truly caused by arsenic binding to proteins through arsenic thiol adhesion? Based on the toxicity order of the experiment, with MMAIII being the most toxic, followed by arsenite, arsenate, DMAV, and MMAV, density functional theory (DFT) calculations can provide a straightforward assessment of this issue. Our practice captures all the transition states associated with a specific imaginary-frequency vibration mode, including proton transfer and simultaneous departure of leaving group. We have obtained the energy barriers for five arsenicals reacting with thiol, alcohol, and amine separately. In addition to energetic favorability, the following are the energy barriers for arsenic's reaction with thiol ranked from low to high: MMAIII (25.4 kcal/mol), arsenite (27.7 kcal/mol), arsenate (32.8 kcal/mol), DMAV (36.2 kcal/mol), and MMAV (38.3 kcal/mol). Results show that the toxicity of arsenicals is mainly caused by their reaction with thiol rather than with alcohol or amine, as supported by the trend of decreasing toxicity and increasing energy barriers. Thus, this DFT calculation may confirm the paradigm that arsenic-thiol adhesion is the primary cause of arsenic toxicity in the body.

Phenothiazine appended thiophene derivative: a trilateral approach to copper ion detection in living cells and aqueous samples

This research paper unveils a fluorescent probe (PTZ-SCN) engineered for the specific detection of Cu2+, featuring a 10-ethyl-10H-phenothiazine-3-carbaldehyde and 2-(thiophen-2-yl) acetonitrile moiety. The fluorescence sensing behavior of PTZ-SCN towards various metal cations was scrutinized in CH3CN : HEPES (9 : 1) buffer aqueous solution. The UV absorbance of PTZ-SCN displayed a distinct red shift in the presence of Cu2+ cations, whereas other metal cations did not cause any interference. Similarly, the fluorescence emission of the probe was also only quenched by Cu2+ cations. The limit of detection (LOD) was calculated as 1.0461 × 10-8 M. PTZ-SCN showed the ability to identify Cu2+ using the colorimetric method, the fluorometric method and even through visual observation in a trilateral detection. We studied the recognition mechanism of PTZ-SCN for Cu2+ using 1H-NMR, HRMS analysis, and time-dependent density functional theory (TDDFT) calculations. Furthermore, our study encompassed the investigation of PTZ-SCN's practical applicability, bridging the gap from research to real-world implementation. This was achieved by employing test strips and water samples for the detection of Cu2+. Additionally, the PTZ-SCN probe's low cytotoxicity and effective imaging properties for Cu2+ in living cells were confirmed, indicating that PTZ-SCN shows the potential to serve as a promising probe for detecting Cu2+in vivo.

Computational Study of Amyloidβ42 Familial Mutations and Metal Interaction: Impact on Monomers and Aggregates Dynamical Behaviors

One of the main hallmarks of Alzheimer's Disease is the formation of β-amyloid plaques, whose formation may be enhanced by metal binding or the appearance of familial mutations. In the present study, the simultaneous effect of familial mutations (E22Q, E22G, E22K, and D23N) and binding to metal ions (Cu(II) or Al(III)) is studied at the Aβ42 monomeric and fibrillar levels. With the application of GaMD and MD simulations, it is observed that the effects of metal binding and mutations differ in the monomeric and fibrillar forms. In the monomeric structures, without metal binding, all mutations reduce the amount of α-helix and increase, in some cases, the β-sheet content. In the presence of Cu(II) and Al(III) metal ions, the peptide becomes less flexible, and the β-sheet content decreases in favor of forming α-helix motifs that stabilize the system through interhelical contacts. Regarding the fibrillar structures, mutations decrease the opening of the fiber in the vertical axis, thereby stabilizing the S-shaped structure of the fiber. This effect is, in general, enhanced upon metal binding. These results may explain the different Aβ42 aggregation patterns observed in familial mutations.

Computational Analysis of the Superoxide Dismutase Mimicry Exhibited by a Zinc(II) Complex with a Redox-Active Organic Ligand

Previously, we found that a Zn(II) complex with the redox-active ligand N-(2,5-dihydroxybenzyl)-N,N',N'-tris(2-pyridinylmethyl)-1,2-ethanediamine (H2qp1) was able to act as a functional mimic of superoxide dismutase, despite its lack of a redox-active transition metal. As the complex catalyzes the dismutation of superoxide to form O2 and H2O2, the quinol in the ligand is believed to cycle between three oxidation states: quinol, quinoxyl radical, and para-quinone. Although the metal is not the redox partner, it nonetheless is essential to the reactivity since the free ligand by itself is inactive as a catalyst. In the present work, we primarily use calculations to probe the mechanism. The calculations support the inner-sphere decomposition of superoxide, suggest that the quinol/quinoxyl radical couple accounts for most of the catalysis, and elucidate the many roles that proton transfer between the zinc complexes and buffer has in the reactivity. Acid/base reactions involving the nonmetal-coordinating hydroxyl group on the quinol are predicted to be key to lowering the energy of the intermediates. We prepared a Zn(II) complex with N-(2-hydroxybenzyl)-N,N',N'-tris(2-pyridinylmethyl)-1,2-ethanediamine (Hpp1) that lacks this functional group and found that it could not catalyze the dismutation of superoxide; this confirms the importance of the second, distal hydroxyl group of the quinol.

The Physical Mechanism of Linear and Nonlinear Optical Properties of Nanographene-Induced Chiral Inversion

Based on density functional theory (DFT) and wave function analysis, the ultraviolet and visible spectrophotometry (UV-Vis) spectra and Raman spectra of 1-meso and 1-rac obtained by the chiral separation of chiral nanographenes are theoretically investigated. The electron excitation properties of 1-meso and 1-rac are studied by means of transition density matrix (TDM) and charge density difference (CDD) diagrams. The intermolecular interaction is discussed based on an independent gradient model based on Hirshfeld partition (IGMH). The interaction of 1-meso and 1-rac with the external environment is studied using the electrostatic potential (ESP), and the electron delocalization degree of 1-meso and 1-rac is studied based on the magnetically induced current under the external magnetic field. Through the chiral separation of 1-rac, two enantiomers, 1-(P, P) and 1-(M, M), were obtained. The electrical-magnetic interaction of the molecule is revealed by analyzing the electron circular dichroism (ECD) spectra of 1-meso, 1-(P, P) and 1-(M, M), the transition electric dipole moment (TEDM) and the transition magnetic dipole moment (TMDM). It is found that 1-(P, P) and 1-(M, M) have opposite chiral properties due to the inversion of the structure.

Stabilization of Naphthalene Diimide Anions by Ion Pair Formation in Nonaqueous Organic Redox Flow Batteries

In redox flow batteries, a compelling strategy for enhancing the charge capacity of redox-active organic molecules involves storing multiple electrons within a single molecule. However, this approach poses unique challenges such as chemical instability by forming radicals, elevated energy requirements, and unsustainable charge concentration. Ion pairing is a possible solution to achieve charge neutrality and engineer redox potential shifts but has received limited attention. In this study, we demonstrate that Li+ can stabilize naphthalene diimide (NDI) anions dissolved in acetonitrile and significantly shift the second cathodic potential close to the first. Our findings, supported by density functional theory calculations and Fourier transform infrared spectroscopy, indicate that dimeric NDI species form stable ion pairs with Li+. Conversely, K+ ions exhibit weak interactions, and cyclic voltammograms confirm significant potential shifts when stronger Lewis acids and solvents with lower donor numbers are employed. Galvanostatic examinations reveal a single voltage plateau with Li+, which indicates a rapid redox process involving doubly charged NDI2- with Li+. These aggregated ion pairs offer the additional benefits of hindering crossover events, contributing to excellent cyclability, and suppressing undesirable side reactions even after 1000 redox cycles.

Macrocyclic Sulfur Ligand Stabilized Trans-Palladium Dichloride Complex: Syntheses, Structure, Chlorine Rotation, and Application in α-Olefination of Nitriles by Primary Alcohols

Herein, we have reported the synthesis of a macrocyclic organosulfur ligand (L1) having a seventeen-membered macrocyclic ring. Subsequently, the corresponding trans-palladium complex (C1) of bulky macrocyclic organosulfur ligand (L1) was synthesized by reacting it with PdCl2 (CH3 CN)2 salt. The newly synthesized ligand and complex were characterized using various analytical and spectroscopic techniques. The complex showed a square planar geometry with trans orientation of two ligands around the palladium center. The complex possesses intramolecular SCH…Cl interactions of 2.648 Å between the macrocyclic ligand and palladium dichloride. The potential energy surface (PES) for the rotational process of C1 suggested a barrier of ~23.81 kcal/mol for chlorine rotation. Furthermore, the bulky macrocyclic organosulfur ligand stabilized palladium complex (C1) was used as a catalyst (2.5 mol %) for α-olefination of nitriles by primary alcohols. The α,β-unsaturated nitrile compounds were found to be the major product of the reaction (57-78 % yield) with broad substrate scope and large functional group tolerance. Notably, the saturated nitrile product was not observed during the reaction. The mechanistic studies suggested the formation of H2 and H2 O as only by-products of the reaction, thereby making the protocol greener and sustainable.

A Simple Electron-Density Based Force Field Model for High-Energy Interactions between Atoms and Molecules

In high-energy molecular dynamics or Monte Carlo simulations, standard force fields optimized for simulations at ambient temperatures are inadequate. This is largely because their repulsive parts have been regarded as not very significant, even well below zero interaction energies. It is, therefore, not obvious which force fields to resort to for simulating hot gases or plasmas. A force field model that uses the electronic densities of noninteracting atoms or molecules within the pair approximation is introduced. We start by deriving a naïve model that neglects any exchange and correlation effects between the electronic clouds and then correct this model by adding a term calibrated from ab initio calculations using the CCSD(T)/cc-pVTZ level of theory. The resulting expression for this term can be regarded as a simple exchange-correlation function. We compare the results for the repulsive part of the potential energy hypersurfaces with the force fields commonly used on some dimers of small molecules.

The photodynamic approach to the molecular-level origin of metal-guided photochromism and ultrafast absorption spectroscopy

Metal-guided photochromic material (photochromic complex) is one of the latest versions of photo-responsive materials due to their smart behaviour and promising real-world applications. The present work explores the molecular-level origin of metal-guided photochromism using a photodynamic approach and ultrafast absorption spectroscopy, to address all existing lacunas. Here, rhodamine B (RhB) dye containing the Schiff base zinc complex is considered a representative photochromic complex for both theoretical treatment and experimental observations. Detailed theoretical studies, including geometry optimization, frontier molecular orbital (FMO) analysis, transition state (TS) identification, and natural bond orbital (NBO) analysis, along with spectral studies, are employed to investigate the photodynamic equilibrium (enol-form keto-form). This equilibrium is regulated by the interplay of intrinsic factors (push-pull effect) and extrinsic factors (such as UV-light, the phenolic-OH group, metal ions, and solvents). The potential energy surface (PES) of the photo-conversion (enol →enol*→keto*→ meta-stable keto) is evaluated. While, the PES of the reversion (meta-stable keto →enol) is constructed based on the studies of thermo-reversion and photo-reversion. Finally, the theoretical findings related to the photodynamic equilibrium are validated by direct experimental evidence obtained through femtosecond transient absorption (fs-TA) spectroscopy.

Molecular hybrids of substituted phenylcarbamoylpiperidine and 1,2,4-triazole methylacetamide as potent 15-LOX inhibitors: Design, synthesis, DFT calculations and molecular docking studies

Inflammation is a multifaceted phenomenon triggered by potentially active mediators acutely released arachidonic acid metabolites partially in lipoxygenase (LOX) pathway which are primarily accountable for causing several diseases in humans. It is widely believed that an inhibitor of the LOX pathway represents a rational approach for designing more potent antiinflammatory leads with druggable super safety profiles. In our continual efforts in search for anti-LOX molecules, the present work was to design a new series of N-alkyl/aralkyl/aryl derivatives (7a-o) of 4-phenyl-5-(1-phenylcarbamoylpiperidine)-4H-1,2,4-triazole-3-thiol which was commenced in seriate formation of phenylcarbamoyl derivative (1), hydrazide (2), semicarbazide (3) and 4-phenyl-5-(1-phenylcarbamoylpiperidine)-4H-1,2,4-triazole-3-thiol (4). The aimed compounds were obtained by reacting 4-phenyl-5-(1-phenylcarbamoylpiperidine)-4H-1,2,4-triazole-3-thiol with assorted N-alkyl/aralkyl/aryl electrophiles. All compounds were characterized by FTIR, 1H-, 13C-NMR spectroscopy, EI-MS and HR-EI-MS spectrometry and screened against soybean 15-LOX for their inhibitory potential using chemiluminescence method. All the compounds except 7m and 7h inhibited the said enzyme remarkably. Compounds 7c,7l, 7j and 7a displayed potent inhibitions ranging from IC50 1.92 ± 0.13 µM to 7.65 ± 0.12 µM. Other analogues 7g, 7o, 7e, 7b, 7d, 7k and 7n revealed excellent inhibitory values ranging from IC50 12.45 ± 0.38 µM to 24.81 ± 0.47 µM. All these compounds did not reveal DPPH radical scavenging activity. Compounds 7i-o maintained > 90 % human blood mononuclear cells (MNCs) viability at 0.125 mM as assayed by MTT whilst others were found toxic. Pharmacokinetic profiles predicted good oral bioavailability and drug-likeness properties of the active scaffolds. SAR investigations showed that phenyl substituted analogue on amide side decreased inhibitory activity due to inductive and mesomeric effects while the mono-alkyl substituted analogues were more active than disubstituted ones and ortho substituted analogues were more potent than meta substituted ones. MD simulation predicted the stability of the 7c ligand and receptor complex as shown by their relative RMSD (root mean square deviation) values. Molecular docking studies displayed hydrogen bonding between the compounds and the enzyme with Arg378 which was common in 7n, 7g, 7h and baicalein. In 7a and quercetin, hydrogen bonding was established through Asn375. RMSD values exhibited good inhibitory profiles in the order quercetin (0.73 Å) < 7 g < baicalein < 7a < 7n < 7 h (1.81 Å) and the binding free energies followed similar pattern. Density functional theory (DFT) data established good correlation between the active compounds and significant activity was associated with more stabilized LUMO (lowest unoccupied molecular orbitals) orbitals. Nevertheless, the present studies declare active analogues like 7c, 7 l, 7a, 7j as leads. Work is ongoing in derivatizing active molecules to explore more effective leads as 15-LOX inhibitors as antiinflammatory agents.

Defective Potassium Poly(Heptazine Imide) Preventing Spin Delocalization and Hole Transfer Deactivation for Efficient Solar Energy Conversion and Storage

Anti-site defective potassium poly(heptazine imide) (KPHI) with the central nitrogen atoms partially replaced by graphitic carbon atoms in the flawed heptazine rings is prepared by direct ionothermal treatment of the rationally designed supramolecular complex in KSCN salt molten. Compared to the KPHIs without the anti-site defect, the anti-site defective KPHI demonstrates significantly improved photocatalytic and dark photocatalytic performances for H2 evolution reaction (HER). In the presence of the hole scavenger, the anti-site defective KPHI exhibits superior photocatalytic stability for HER lasting 20 h, whereas the deactivation is observed from the ordinary KHPIs after 3 h HER. Moreover, the H2 yield in the dark by the stored photoelectrons in the anti-site defective KPHI increases by more than an order of magnitude. Density functional theory calculations reveal that the anti-site defective unit in KPHI not only prevents spin delocalization but also inhibits the deactivation of hole transfer, which are beneficial to photoelectron storage and photocatalytic activity. The findings in this study provide insight into the photophysical and catalytic properties of KPHI, which conclude a strategy to improve the performances for solar energy conversion and storage by incorporating intrinsic anti-site defects in KPHI.

Molecular modelling of fullerene C60 functionalized by nitric oxide for use in biological environment

The unique potential of fullerene C60 for various biological applications has ignited significant interest. However, its inherent non-polarity poses a critical challenge for its effective integration within biological systems. This study delves into the intricate physicochemical characteristics of the innovative [C60 + NO] complex using density functional theory and time-dependent density functional theory. The computational analyses encompass molecular charge, surface electrostatic potential, and dipole moment evaluations. Impressively, the dipole moment of the [C60 + NO] complex significantly increases to 12.92 D. Meticulous surface analysis reveals a subtle interplay between molecular structures, indicating weak interactions. The analysis of the absorption spectrum unveils a noteworthy red-shift of 200 nm subsequent to complex formation. To elucidate the electron transfer mechanisms, we explore photo-induced electron transfer through CAM-B3LYP. This exploration elucidates intricate pathways governing electron transfer, with complementary insights gleaned from Marcus theory's outputs, especially the Gibbs free energy of electron transfer. Changes in the physicochemical properties of approaching C60 and NO molecules reveal interesting results compared to separate molecules. These findings resonate profoundly in the context of potential biological and pharmaceutical utilization. With implications for the biomedical area, the outcomes linked to the [C60 + NO] complex kindle optimism for pioneering biomedical applications.

Photoswitchable Photochromic Chelating Spironaphthoxazines: Synthesis, Photophysical Properties, Quantum-Chemical Calculations, and Complexation Ability

The stable and efficient photochromic and photoswitchable molecular systems designed from spirooxazines are of increasing scientific and practical interest because of their present and future applications in advanced technologies. Among these compounds, chelating spironaphthoxazines have received widespread attention due to their efficient optical response after complexation with some metal ions being of biomedical interest and environmental importance, as well as their good cycle performance and high reliability, especially by metal ion sensing. In this mini-review, we summarize our results in the design of novel photoswitchable chelating spironaphthoxazines with specific substituents in their naphthoxazine or indoline ring systems in view of recent progress in the development of such molecular systems and their applications as metal ion sensors. The design, synthesis methods, and photoresponse of such spirooxazine derivatives relevant to their applications, as well as quantum-chemical calculations for these compounds, are presented. Examples of various design concepts are discussed, such as sulfobutyl, hydroxyl, benzothiazolyl, or ester and carboxylic acid as substituents in the chelating spironaphthoxazine molecules. Further developments and improvements of this interesting and promising kind of molecular photoswitches are outlined.

First-Principles Study on the Selective Separation of Toxic Gases by Mg-MOF-74

This study primarily focused on the detection and separation of toxic gases such as CO, H2S, SO2, NH3, NO, and NO2 by Mg-MOF-74, as well as assessing the stability of those toxic gases on it. The calculations were performed by using density functional theory as implemented in the Gaussian-09 and Quantum ESPRESSO suites of the program. GGA-type PBE-D2 functionals with a plane wave basis set were used in the optimization of the Mg-MOF-74 crystal, and hybrid-type B3LYP and M06 functionals with the 6-31G*basis set were used in cluster calculation. The binding energies of CO and H2S with MOF were found to be in the physisorption range, whereas the energies of SO2, NH3, NO, and NO2 were found to be in the chemisorption range. Based on binding energy, hardness, and softness studies, it was found that NO and NO2 molecules were more stable in Mg-MOF-74, suggesting that Mg-MOF-74 is a good detector for NO and NO2 molecules.

In Silico Study of Camptothecin-Based Pro-Drugs Binding to Human Carboxylesterase 2

Pro-drugs, which ideally release their active compound only at the site of action, i.e., in a cancer cell, are a promising approach towards an increased specificity and hence reduced side effects in chemotherapy. A popular form of pro-drugs is esters, which are activated upon their hydrolysis. Since carboxylesterases that catalyse such a hydrolysis reaction are also abundant in normal tissue, it is of great interest whether a putative pro-drug is a probable substrate of such an enzyme and hence bears the danger of being activated not just in the target environment, i.e., in cancer cells. In this work, we study the binding mode of carboxylesters of the drug molecule camptothecin, which is an inhibitor of topoisomerase I, of varying size to human carboxylesterase 2 (HCE2) by molecular docking and molecular dynamics simulations. A comparison to irinotecan, known to be a substrate of HCE2, shows that all three pro-drugs analysed in this work can bind to the HCE2 protein, but not in a pose that is well suited for subsequent hydrolysis. Our data suggest, moreover, that for the irinotecan substrate, a reactant-competent pose is stabilised once the initial proton transfer from the putative nucleophile Ser202 to the His431 of the catalytic triad has already occurred. Our simulation work also shows that it is important to go beyond the static models obtained from molecular docking and include the flexibility of enzyme-ligand complexes in solvents and at a finite temperature. Under such conditions, the pro-drugs studied in this work are unlikely to be hydrolysed by the HCE2 enzyme, indicating a low risk of undesired drug release in normal tissue.

Internal conversion induced by external electric and magnetic fields

We have developed a new methodology for calculating contributions to the rate constants (kIC) of internal conversion that are induced by external electric (kIC-E) or magnetic (kIC-M) fields. The influence of the external electric and magnetic fields on the kIC was estimated for seven representative molecules. We show that the kIC-E contribution calculated at a field strength of 1011 V m-1 is generally as large as the kIC rate constant in the absence of the external field. For indocyanine green, azaoxa[8]circulene, and pyromitene 567, the kIC-E contribution is as large as kIC already at a field strength of 109 V m-1. Such electric-field strengths occur for example in plasmonic studies and in strong laser-field experiments. The induced effect on the kIC rate constant should be accounted for in calculations of photophysical properties of molecules involved in such experiments. The induced effect of an external magnetic field on kIC can be neglected in experiments on Earth because the magnetic contribution becomes significant only at very strong magnetic fields of 104-105 T that cannot be achieved on Earth. However, the magnetic effect on the rate constant of internal conversion can be important in astrophysical studies, where extremely strong magnetic fields occur near neutron stars and white dwarfs.

Spin canting and slow magnetic relaxation in mononuclear cobalt(II) sulfadiazine ternary complexes

Monomeric [Co(SDZ)2phen] (1) and [Co(SDZ)(bq)Cl] (2) complexes (SDZ = sulfadiazine, phen = 1,10-phenanthroline, and bq = 2,2'-biquinoline) have been synthesized and characterized. X-ray diffraction studies indicate that SDZ acts as a bidentate ligand coordinating through the sulfonamide and the pyrimidine N atoms in both compounds. In complex 1, the coordination sphere consists of two SDZ ligands and a bis-chelating phen ligand, giving rise to a CoN6 coordination sphere. On the other hand, 2 has a CoN4Cl core, with two N-atoms from SDZ and two from the bq ligand. Both compounds have been studied by dc and ac magnetometry and shown to display slow magnetic relaxation under an optimum external dc field (1 kOe) at low temperatures. Moreover, compound 2 displays long range magnetic ordering provided by spin-canted antiferromagnetism, which has been characterized by further field-dependent magnetic susceptibility measurements, FC/ZFC curves, hysteresis loops and frequency-independent ac curves. The signs of the calculated D parameters, positive in 1 and negative in 2, have been rationalized according to the two lowest-lying transitions in the orbital energy diagrams derived from ab initio ligand field theory (AILFT). In a subsequent attempt to reveal the possible hidden zero-field SMM behaviour, Ni(II)-based 3 and Co(II)-doped Ni(II)-based (with a Ni : Co ratio of 0.9 : 0.1) heterometallic compound 2Ni were synthesized.

Nano-size cobalt-doped cerium oxide particles embedded into graphitic carbon nitride for enhanced electrochemical sensing of insecticide fenitrothion in environmental samples: An experimental study with the theoretical elucidation of redox events

In the present work, a nanocomposite, based on embedding Co-doped CeO2 nanoparticles into graphitic carbon nitride (g-C3N4), was applied to functionalize commercial glassy carbon paste. This is the first application of the electrochemical sensor, developed through the proposed procedure, in electrochemical sensing. The sensor was utilized for the electrochemical determination of organophosphate pesticide fenitrothion (FNT). Cyclic voltammetry identified reversible oxidation of FNT (oxidation at 0.18 V and reduction at 0.13 V) and additional reduction at -0.62 V vs. Ag/AgCl in HCl solution (pH = 1). Theoretical calculations were carried out to model and elucidate experimentally observed redox processes. Special attention was devoted to modeling experimental conditions, and based on the obtained results, a detailed redox mechanism of the investigated analyte was proposed. This represents the first complete and unambiguous elucidation of the FNT redox mechanism, supported by joined experimental and theoretical data. Square wave voltammetry (SWV) was utilized for quantification, whereby the FNT oxidation peak was chosen for monitoring the analyte concentration. The developed sensor provided a nanomolar detection limit (3.2 nmol L-1), a wide linear concentration range (from 0.01 to 13.7 μmol L-1), and good precision, repeatability, and selectivity towards FNT. Practical application possibility was explored by testing the sensor performance for examining tap water and apple samples. Recovery tests, conducted during the FNT-spiked sample assays, showed a great application capability of the developed sensor for real-time monitoring of FNT traces in environmental samples.