How does basis set superposition error change the potential surfaces for hydrogen‐bonded dimers?

Avian cryptochrome 4 binds superoxide

Flavin-binding cryptochromes are blue-light sensitive photoreceptors that have been implicated with magnetoreception in some species. The photocycle involves an intra-protein photo-reduction of the flavin cofactor, generating a magnetosensitive radical pair, and its subsequent re-oxidation. Superoxide (O2 • - ) is generated in the re-oxidation with molecular oxygen. The resulting O2 • - -containing radical pairs have also been hypothesised to underpin various magnetosensitive traits, but due to fast spin relaxation when tumbling in solution would require immobilisation. We here describe our insights in the binding of superoxide to cryptochrome 4 from C. livia based on extensive all-atom molecular dynamics studies and density-functional theory calculations. The positively charged "crypt" region that leads to the flavin binding pocket transiently binds O2 • - at 5 flexible binding sites centred on arginine residues. Typical binding times amounted to tens of nanoseconds, but exceptional binding events extended to several hundreds of nanoseconds and slowed the rotational diffusion, thereby realising rotational correlation times as large as 1 ns. The binding sites are particularly efficient in scavenging superoxide escaping from a putative generation site close to the flavin-cofactor, possibly implying a functional relevance. We discuss our findings in view of a potential magnetosensitivity of biological flavin semiquinone/superoxide radical pairs.

Intermolecular interactions between malvidin-3-O-glucoside and caffeic acid: Structural and thermodynamic characterization and its effect on real wine color quality

The copigmentation effect between malvidin-3-O-glucoside and caffeic acid was comprehensive inquiry on the model wine solution, theoretical simulation and real wine. Thermodynamic parameters were determined by UV/Visible spectroscopy and Isothermal titration calorimetry (ITC). Theoretical data were obtained employing a dispersion-corrected density functional approach. The effects in real wines were investigated by adding the caffeic acid during different fermentation periods. Results shown that the copigmentation reaction between caffeic acid and malvidin-3-O-glucoside is a spontaneous exothermic reaction driven by hydrogen bonding and dispersions forces. Computations show that the polyhydroxyl sugar moiety and phenolic hydroxyl groups are the key active sites. The addition of caffeic acid in post-alcohol fermentation samples evidences an improving color characteristics in the wine.

Strategies to Obtain Reliable Energy Landscapes from Embedded Multireference Correlated Wavefunction Methods for Surface Reactions

Embedded correlated wavefunction (ECW) theory is a powerful tool for studying ground- and excited-state reaction mechanisms and associated energetics in heterogeneous catalysis. Several factors are important to obtaining reliable ECW energies, critically the construction of consistent active spaces (ASs) along reaction pathways when using a multireference correlated wavefunction (CW) method that relies on a subset of orbital spaces in the configuration interaction expansion to account for static electron correlation, e.g., complete AS self-consistent field theory, in addition to the adequate partitioning of the system into a cluster and environment, as well as the choice of a suitable basis set and number of states included in excited-state simulations. Here, we conducted a series of systematic studies to develop best-practice guidelines for ground- and excited-state ECW theory simulations, utilizing the decomposition of NH3 on Pd(111) as an example. We determine that ECW theory results are relatively insensitive to cluster size, the aug-cc-pVDZ basis set provides an adequate compromise between computational complexity and accuracy, and that a fixed-clean-surface approximation holds well for the derivation of the embedding potential. Additionally, we demonstrate that a merging approach, which involves generating ASs from the molecular fragments at each configuration, is preferable to a creeping approach, which utilizes ASs from adjacent structures as an initial guess, for the generation of consistent potential energy curves involving open-d-shell metal surfaces, and, finally, we show that it is essential to include bands of excited states in their entirety when simulating excited-state reaction pathways.

Insights into Cis-Amide-Modified Carbon Nanotubes for Selective Purification of CH4 and H2 from Gas Mixtures: A Comparative DFT Study

Among a plethora of mixtures, the methane (CH4) and hydrogen (H2) mixture has garnered considerable attention for multiple reasons, especially in the framework of energy production and industrial processes as well as ecological considerations. Despite the fact that the CH4/H2 mixture performs many critical tasks, the presence of other gases, such as carbon dioxide, sulfur compounds like H2S, and water vapor, leads to many undesirable consequences. Thus purification of this mixture from these gases assumes considerable relevance. In the current research, first-principle calculations in the frame of density functional theory are carried out to propose a new functional group for vertically aligned carbon nanotubes (VA-CNTs) interacting preferentially with polar molecules rather than CH4 and H2 in order to obtain a more efficient methane and hydrogen separations The binding energies associated with the interactions between several chemical groups and target gases were calculated first, and then a functional group formed by a modified ethylene glycol and acetyl amide was selected. This functional group was attached to the CNT edge with an appropriate diameter, and hence the binding energies with the target gases and steric hindrance were evaluated. The binding energy of the most polar molecule (H2O) was found to be more than six times higher than that of H2, indicating a significant enhancement of the nanotube tip's affinity toward polar gases. Thus, this functionalization is beneficial for enhancing the capability of highly packed functionalized VA-CNT membranes to purify CH4/H2 gas mixtures.

Probing the Effects of Size and Charge on the Monohydration and Dihydration of SiF5- and SiF62- via Comparisons with BF4- and PF6. J Phys Chem A 2024;128:5637-5645. [PMID: 38976798 DOI: 10.1021/acs.jpca.4c03430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

This study systematically examines the interactions of the trigonal bipyramidal silicon pentafluoride and octahedral silicon hexafluoride anions with either one or two water molecules, (SiF5-(H2O)n and SiF62-(H2O)n, respectively, where n = 1, 2). Full geometry optimizations and subsequent harmonic vibrational frequency computations are performed using the CCSD(T) ab initio method with a triple-ζ correlation consistent basis set augmented with diffuse functions on all non-hydrogen atoms (cc-pVTZ for H and aug-cc-pVTZ for Si, O, and F; denoted as haTZ). Two monohydrate and six dihydrate minima have been identified for the SiF5-(H2O)n systems, whereas one monohydrate and five dihydrate minima have been identified for the SiF62-(H2O)n systems. Both monohydrated anions have a minimum in which the water molecule adopts a symmetric double ionic hydrogen bond (DIHB) motif with C2v symmetry. However, a second unique monohydrate minimum has been identified for SiF5- in which the water molecule adopts an asymmetric DIHB motif along the edge of the trigonal bipyramidal anion between one axial and one equatorial F atom. This Cs structure is more than 2 kcal mol-1 lower in energy than the C2v local minimum at the CCSD(T)/haTZ level of theory. While the interactions between the solvent and ionic solute are quite strong for the monohydrated anions (electronic dissociation energies of ≈12 and ≈24 kcal mol-1 for the SiF5-(H2O)1 and SiF62-(H2O)1 global minima, respectively), these values are nearly perfectly doubled for the dihydrates, with the lowest-energy SiF5-(H2O)2 and SiF62-(H2O)2 minima exhibiting dissociation energies of ≈24 and ≈47 kcal mol-1, respectively. Structures that form hydrogen bonds between the solvating water molecules also exhibit the largest shifts in the harmonic OH stretching frequencies for the waters of hydration. These shifts can exceed -100 cm-1 for the SiF5-(H2O)2 minimum and -300 cm-1 for the SiF62-(H2O)2 minimum relative to an isolated H2O molecule at the CCSD(T)/haTZ level of theory. This work also corrects the OH stretching frequency shifts for two dihydrate minima of PF6- that were previously erroneously reported ( J. Phys. Chem. A 2020, 124, 8744-8752, DOI: 10.1021/acs.jpca.0c06466).

Gallic acid improves color quality and stability of red wine via physico-chemical interaction and chemical transformation as revealed by thermodynamics, real wine dynamics and benchmark quantum mechanical calculations

The aim of this study was to explore the copigmentation effect of gallic acid on red wine color and to dissect its mechanism at the molecular level. Three-dimensional studies, e.g., in model wine, in real wine and in silico, and multiple indicators, e.g., color, spectrum, thermodynamics and phenolic dynamics, were employed. The results showed that gallic acid significantly enhanced the color quality and stability of red wine. Physico-chemical interactions and chemical transformations should be the most likely mechanism, and physico-chemical interactions are also a prerequisite for chemical transformations. QM calculations of the physico-chemical interactions proved that the binding between gallic acid and malvidin-3-O-glucoside is a spontaneous exothermic reaction driven by hydrogen bonding and dispersion forces. The sugar moiety of malvidin-3-O-glucoside and the phenolic hydroxyl groups of gallic acid affect the formation of hydrogen bonds, while the dispersion interaction was related to the stacking of the molecular skeleton.

Base-pairing of uracil and 2,6-diaminopurine: from cocrystals to photoreactivity

We show that the non-canonical nucleobase 2,6-diaminopurine (D) spontaneously base pairs with uracil (U) in water and the solid state without the need to be attached to the ribose-phosphate backbone. Depending on the reaction conditions, D and U assemble in thermodynamically stable hydrated and anhydrated D-U base-paired cocrystals. Under UV irradiation, an aqueous solution of D-U base-pair undergoes photochemical degradation, while a pure aqueous solution of U does not. Our simulations suggest that D may trigger the U photodimerization and show that complementary base-pairing modifies the photochemical properties of nucleobases, which might have implications for prebiotic chemistry.

Unveiling the chemical kinetics of aminomethanol (NH2CH2OH): insights into O . H and O2 photo-oxidation reactions and formamide dominance

Aminomethanol is released into the atmosphere through various sources, including biomass burning. In this study, we have expounded the chemical kinetics of aminomethanol in the reaction pathways initiated by the hydroxyl radical (O ˙ H) with the aid of ab initio//density functional theory (DFT) i.e., coupled-cluster theory (CCSD(T))//hybrid-DFT (M06-2X/6-311++G (3df, 3pd). We have explored various possible directions of theO ˙ H radical on aminomethanol, as well as the formation of distinct pre-reactive complexes. Our computational findings reveal that the H transfer necessitates activation energies ranging from 4.1 to 6.5 kcal/mol from the -CH2 group, 3.5-6.5 kcal/mol from the -NH2 group and 7-9.3 kcal/mol from the -OH group of three rotational conformers. The H transfer from -CH2, -NH2 and -OH exhibits an estimated total rate constant (k OH) of approximately 1.97 × 10-11 cm3 molecule-1 s-1 at 300 K. The branching fraction analysis indicates a pronounced dominance of C-centered NH2C ˙ HOH radicals with a favorability of 77%, surpassing the N-centeredN ˙ HCH2OH (20%) and O-centered NH2CH2O ˙ (3%) radicals. Moreover, our investigation delves into the oxidation of the prominently favored carbon-centered NH2C ˙ HOH radical through its interaction with atmospheric oxygen molecules. Intriguingly, our findings reveal that formamide (NH2CHO) emerges as the predominant product in the NH2C ˙ HOH + 3O2 reaction, eclipsing alternative outcomes such as amino formic acid (NH2COOH) and formimidic acid (HN = C(H)-OH). At atmospheric conditions pertinent to the troposphere, the branching fraction value for the formation of formamide is about 99%, coupled with a rate constant of 5.5 × 10-12 cm3 molecule-1 s-1. Finally, we have scrutinized the detrimental impact of formamide on the atmosphere. Interaction of formamide with atmospheric hydroxyl radicals could give rise to the production of potentially perilous compounds such as HNCO. Further, unreactedN ˙ HCH2OH radicals may initiate the formation of carcinogenic nitrosamines when reacting with trace N-oxides (namely, NO and NO2). This, in turn, escalates the environmental risk factors.

Weakly bound complexes of 1,2,3-triazole with nitrogen and carbon dioxide isolated in solid argon: A combined FT-IR matrix isolation and theoretical investigation

Matrix isolation FT-IR spectroscopy was combined with quantum-chemical calculations in order to characterize complexes of 1,2,3-triazole (3TR) with nitrogen and carbon dioxide. Geometries of the possible 1:1 and 1:2 complexes, as well as 3TR dimers, were optimized at the DFT (B3LYP-D3) level of theory with the 6-311++G(3df,3pd) basis set. Six different 3TR⋯N2 structures of the 1:1 stoichiometry were optimized which are characterized by weak hydrogen bonds (N-H⋯N and C-H⋯N) and/or Van der Waals type interactions (N⋯C, N⋯N, N⋯π). Two the most stable geometries, both containing a N-H⋯N bridge, were identified experimentally in solid argon. As for 3TR⋯CO2 complexes, out of two minima located on the potential energy surface, only one with a strongly bent N-H⋯O hydrogen bond was detected in the matrix after deposition. In both cases, only annealing experiments at 32 K resulted in the formation of small amounts of 1:2 structures.

Probing Ion-Receptor Interactions in Halide Complexes of Octamethyl Calix[4]Pyrrole

Ion receptors are molecular hosts that bind ionic guests, often with great selectivity. The interplay of solvation and ion binding in anion host-guest complexes in solution governs the binding efficiency and selectivity of such ion receptors. To gain molecular-level insight into the intrinsic binding properties of octamethyl calix[4]pyrrole (omC4P) host molecules with halide guest ions, we performed cryogenic ion vibrational spectroscopy (CIVS) of omC4P in complexes with fluoride, chloride, and bromide ions. We interpret the spectra using density functional theory, describing the infrared spectra of these complexes with both harmonic and anharmonic second-order vibrational perturbation theory (VPT2) calculations. The NH stretching modes of the pyrrole moieties serve as sensitive probes of the ion binding properties, as their frequencies encode the ion-receptor interactions. While scaled harmonic spectra reproduce the experimental NH stretching modes of the chloride and bromide complexes in broad strokes, the high proton affinity of fluoride introduces strong anharmonic effects. As a result, the spectrum of F-·omC4P is not even qualitatively captured by harmonic calculations, but it is recovered very well by VPT2 calculations. In addition, the VPT2 calculations recover the intricate coupling of the NH stretching modes with overtones and combination bands of CH stretching and NH bending modes and with low-frequency vibrations of the omC4P macrocycle, which are apparent for all of the halide ion complexes investigated here. A comparison of the CIVS spectra with infrared spectra of solutions of the same ion-receptor complexes in d3-acetonitrile and d6-acetone shows how ion solvation changes the ion-receptor interactions for the different halide ions.

Acyl Capping Group Identity Effects on α-Helicity: On the Importance of Amide·Water Hydrogen Bonds to α-Helix Stability

Acyl capping groups stabilize α-helices relative to free N-termini by providing one additional C═Oi···Hi+4-N hydrogen bond. The electronic properties of acyl capping groups might also directly modulate α-helix stability: electron-rich N-terminal acyl groups could stabilize the α-helix by strengthening both i/i + 4 hydrogen bonds and i/i + 1 n → π* interactions. This hypothesis was tested in peptides X-AKAAAAKAAAAKAAGY-NH2, where X = different acyl groups. Surprisingly, the most electron-rich acyl groups (pivaloyl and iso-butyryl) strongly destabilized the α-helix. Moreover, the formyl group induced nearly identical α-helicity to that of the acetyl group, despite being a weaker electron donor for hydrogen bonds and for n → π* interactions. Other acyl groups exhibited intermediate α-helicity. These results indicate that the electronic properties of the acyl carbonyl do not directly determine the α-helicity in peptides in water. In order to understand these effects, DFT calculations were conducted on α-helical peptides. Using implicit solvation, α-helix stability correlated with acyl group electronics, with the pivaloyl group exhibiting closer hydrogen bonds and n → π* interactions, in contrast to the experimental results. However, DFT and MD calculations with explicit water solvation revealed that hydrogen bonding to water was impacted by the sterics of the acyl capping group. Formyl capping groups exhibited the closest water-amide hydrogen bonds, while pivaloyl groups exhibited the longest. In α-helices in the PDB, the highest frequency of close amide-water hydrogen bonds is observed when the N-cap residue is Gly. The combination of experimental and computational results indicates that solvation (hydrogen bonding of water) to the N-terminal amide groups is a central determinant of α-helix stability.

Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms

Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant unusually preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employ static and dynamic structural methods and observe that, compared to R132H, the R132Q active site adopts a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling reveals a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.

Tethered Helical Ladder-Type Aromatic Lactams

Tethered nonplanar aromatics (TNAs) make up an important class of nonplanar aromatic compounds showing unique features. However, the knowledge on the synthesis, structures, and properties of TNAs remains insufficient. In this work, a new type of TNAs, the tethered aromatic lactams, is synthesized via Pd-catalyzed consecutive intramolecular direct arylations. These molecules possess a helical ladder-type conjugated system of up to 13 fused rings. The overall yields ranged from 3.4 to 4.3%. The largest of the tethered aromatic lactams, 6L-Bu-C14, demonstrates a guest-adaptive hosting capability of TNAs for the first time. When binding fullerene guests, the cavity of 6L-Bu-C14 became more circular to better accommodate spherical fullerene molecules. The host-guest interaction is thoroughly studied by X-ray crystallography, theoretical calculations, fluorescence titration, and nuclear magnetic resonance (NMR) titration experiments. 6L-Bu-C14 shows stronger binding with C70 than with C60 due to the better convex-concave π-π interaction. P and M enantiomers of all tethered aromatic lactams show distinct and persistent chiroptical properties and demonstrate the potential of chiral TNAs as circularly polarized luminescence (CPL) emitters.

Generation and reactivity of the fragment ion [B12I8S(CN)]- in the gas phase and on surfaces

Gaseous fragment ions generated in mass spectrometers may be employed as "building blocks" for the synthesis of novel molecules on surfaces using ion soft-landing. A fundamental understanding of the reactivity of the fragment ions is required to control bond formation of deposited fragments in surface layers. The fragment ion [B12X11]- (X = halogen) is formed by collision-induced dissociation (CID) from the precursor [B12X12]2- dianion. [B12X11]- is highly reactive and ion soft-landing experiments have shown that this ion binds to the alkyl chains of organic molecules on surfaces. In this work we investigate whether specific modifications of the precursor ion affect the chemical properties of the fragment ions to such an extent that attachment to functional groups of organic molecules on surfaces occurs and binding of alkyl chains is prevented. Therefore, a halogen substituent was replaced by a thiocyanate substituent. CID of the precursor [B12I11(SCN)]2- ion preferentially yields the fragment ion [B12I8S(CN)]-, which shows significantly altered reactivity compared to the fragment ions of [B12I12]2-. [B12I8S(CN)]- has a previously unknown structural element, wherein a sulfur atom bridges three boron atoms. Gas-phase reactions with different neutral reactants (cyclohexane, dimethyl sulfide, and dimethyl amine) accompanied by theoretical studies indicate that [B12I8S(CN)]- binds with higher selectivity to functional groups of organic molecules than fragment ions of [B12I12]2- (e.g., [B12I11]- and [B12I9]-). These findings were further confirmed by ion soft-landing experiments, which showed that [B12I8S(CN)]- ions attacked ester groups of adipates and phthalates, whereas [B12I11]- ions only bound to alkyl chains of the same reagents.

Repulsive Lateral Interaction of Water Molecules at the Initial Stages of Adsorption in Microporous AlPO4-11 According to 27Al NMR and DFT

Lateral (adsorbate-adsorbate) interactions between adsorbed molecules affect various physical and chemical properties of microporous adsorbents and catalysts, influencing their functional properties. In this work, we studied the hydration of microporous AlPO4-11 aluminophosphate, which has an unusually ordered structure upon adsorption of water vapor, and according to 27Al NMR data, only tetrahedrally or octahedrally coordinated Al sites are present in the AlPO4-11. These 27Al NMR data are consistent with the results of density functional theory (DFT) calculations of hydrated AlPO4-11, which revealed the presence of a strong repulsive lateral interaction at the initial stage of adsorption, suppressing the adsorption of water on neighboring (separated by one -O-P-O- bridge) Al crystallographic sites. As a result, of all the different aluminum sites, only half of the Al1 sites adsorb two water molecules and acquire octahedral coordination.

An Atomic-Level Perspective on the interactions between Organic Pollutants and PET particles: A Comprehensive Computational Investigation

Microplastics (MPs) have recently attracted a lot of attention worldwide due to their abundance and potentially harmful effects on the environment and on human health. One of the factors of concern is their ability to adsorb and disperse other harmful organic pollutants in the environment. To properly assess the adsorption capacity of MP for organic pollutants in different environments, it is pivotal to understand the mechanisms of their interactions in detail at the atomic level. In this work, we studied interactions between polyethylene terephthalate (PET) MP and small organic pollutants containing different functional groups within the framework of density functional theory (DFT). Our computational outcomes show that organic pollutants mainly bind to the surface of a PET model via weak non-bonding interactions, mostly hydrogen bonds. The binding strength between pollutant molecules and PET particles strongly depends on the adsorption site while we have found that the particle size is of lesser importance. Specifically, carboxylic sites are able to form strong hydrogen bonds with pollutants containing hydrogen bond donor or acceptor groups. On the other hand, it is found that in such kind of systems π-π interactions play a minor role in adsorption on PET particles.

Spectrally Resolved and Highly Parallelized Raman Difference Spectroscopy for the Analysis of Drug-Target Interactions between the Antimalarial Drug Chloroquine and Hematin

Malaria is a severe disease caused by cytozoic parasites of the genus Plasmodium, which infiltrate and infect red blood cells. Several drugs have been developed to combat the devastating effects of malaria. Antimalarials based on quinolines inhibit the crystallization of hematin into hemozoin within the parasite, ultimately leading to its demise. Despite the frequent use of these agents, there are unanswered questions about their mechanisms of action. In the present study, the quinoline chloroquine and its interaction with the target structure hematin was investigated using an advanced, highly parallelized Raman difference spectroscopy (RDS) setup. Simultaneous recording of the spectra of hematin and chloroquine mixtures with varying compositions enabled the observation of changes in peak heights and positions based on the altered molecular structure resulting from their interaction. A shift of (-1.12 ± 0.05) cm-1 was observed in the core-size marker band ν(CαCm)asym peak position of the 1:1 chloroquine-hematin mixture compared to pure hematin. The oxidation-state marker band ν(pyrrole half-ring)sym exhibited a shift by (+0.93 ± 0.13) cm-1. These results were supported by density functional theory (DFT) calculations, indicating a hydrogen bond between the quinolinyl moiety of chloroquine and the oxygen atom of ferric protoporphyrin IX hydroxide (Fe(III)PPIX-OH). The consequence is a reduced electron density within the porphyrin moiety and an increase in its core size. This hypothesis provided further insights into the mechanism of hemozoin inhibition, suggesting chloroquine binding to the monomeric form of hematin, thereby preventing its further crystallization to hemozoin.

New Aspects of Alcohol-Alcohol and Alcohol-Water Interactions: Crystallographic and Quantum Chemical Studies of Antiparallel O-H/O-H Interactions

New modes of interaction, antiparallel O-H/O-H interactions of alcohol-alcohol dimers and alcohol-water dimers, were studied by analyzing data in the Cambridge Structural Database (CSD) and by calculating potential energy surfaces at a very accurate quantum chemical CCSD(T)/CBS level. The data reveal the existence of antiparallel interactions in crystal structures and significant interaction energies. Data from the CSD for alcohol-alcohol dimers show 49.2% of contacts with classical hydrogen bonds and 10.1% of contacts with antiparallel interactions, while for alcohol-water dimers, 59.4% of contacts are classical hydrogen bonds and only 0.6% of contacts are antiparallel interactions. The calculations were performed on methanol, ethanol, and n-propanol dimers. Classical hydrogen-bonded alcohol-alcohol and alcohol-water dimers have interaction energies of up to -6.2 kcal/mol and up to -5.5 kcal/mol, respectively. Antiparallel interactions in alcohol-alcohol and alcohol-water dimers have interaction energies of up to -4.7 kcal/mol and up to -4.4 kcal/mol, respectively. Symmetry-adapted perturbation theory analysis for antiparallel interactions shows their electrostatic nature.

Exploring borderline SN1-SN2 mechanisms: the role of explicit solvation protocols in the DFT investigation of isopropyl chloride

Nucleophilic substitution at saturated carbon is a crucial class of organic reactions, playing a pivotal role in various chemical transformations that yield valuable compounds for society. Despite the well-established SN1 and SN2 mechanisms, secondary substrates, particularly in solvolysis reactions, often exhibit a borderline pathway. A molecular-level understanding of these processes is fundamental for developing more efficient chemical transformations. Typically, quantum-chemical simulations of the solvent medium combine explicit and implicit solvation methods. The configuration of explicit molecules can be defined through top-down approaches, such as Monte Carlo (MC) calculations for generating initial configurations, and bottom-up methods that involve user-dependent protocols to add solvent molecules around the substrate. Herein, we investigated the borderline mechanism of the hydrolysis of a secondary substrate, isopropyl chloride (iPrCl), at DFT-M06-2X/aug-cc-pVDZ level, employing explicit and explicit + implicit protocols. Top-down and bottom-up approaches were employed to generate substrate-solvent complexes of varying number (n = 1, 3, 5, 7, 9, and 12) and configurations of H2O molecules. Our findings consistently reveal that regardless of the solvation approach, the hydrolysis of iPrCl follows a loose-SN2-like mechanism with nucleophilic solvent assistance. Increasing the water cluster around the substrate in most cases led to reaction barriers of ΔH‡ ≈ 21 kcal mol-1, with nine water molecules from MC configurations sufficient to describe the reaction. The More O'Ferrall-Jencks plot demonstrates an SN1-like character for all transition state structures, showing a clear merged profile. The fragmentation activation strain analyses indicate that energy barriers are predominantly controlled by solvent-substrate interactions, supported by the leaving group stabilization assessed through CHELPG atomic charges.

Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms

Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant uniquely preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employed static and dynamic structural methods and found that, compared to R132H, the R132Q active site adopted a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling revealed a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.

An integrated experimental and theoretical approach to probe Cr(vi) uptake using decorated halloysite nanotubes for efficient water treatment

Halloysite nanotubes (HNTs) were surface functionalized using four distinct chemical moieties (amidoxime, hydrazone, ethylenediamine (EDA), and diethylenetriamine (DETA)), producing modified HNTs (H1-H4) capable of binding with Cr(vi) ions. Advanced techniques like FTIR, XRD, SEM, and EDX provided evidence of the successful functionalization of these HNTs. Notably, the functionalization occurred on the surface of HNTs, rather than within the interlayer or lumen. These decorated HNTs were effective in capturing Cr(vi) ions at optimized sorption parameters, with adsorption rates ranging between 58-94%, as confirmed by atomic absorption spectroscopy (AAS). The mechanism of adsorption was further scrutinized through the Freundlich and Langmuir isotherms. Langmuir isotherms revealed the nearest fit to the data suggesting the monolayer adsorption of Cr(vi) ions onto the nanotubes, indicating a favorable adsorption process. It was hypothesized that Cr(vi) ions are primarily attracted to the amine groups on the modified nanotubes. Quantum chemical calculations further revealed that HNTs functionalized with hydrazone structures (H2) demonstrated a higher affinity (interaction energy -26.33 kcal mol-1) for the Cr(vi) ions. This can be explained by the formation of stronger hydrogen bonds with the NH moieties of the hydrazone moiety, than those established by the OH of oxime (H1) and longer amine chains (H3 and H4), respectively. Overall, the findings suggest that these decorated HNTs could serve as an effective and cost-efficient solution for treating water pollution.

Energy landscape of perylenediimide chromophoric aggregates

Understanding the self-assembly of conjugated organic materials at the molecular level is crucial in their potential applications as active components in electronic and optoelectronic devices. The type of aggregation significantly influences the intriguing electronic and optical characteristics differing from their constituent molecules. Perylenediimides (PDIs), electron-deficient molecules exhibiting remarkable n-type semiconducting properties, are among the most explored organic fluorescent materials due to their high fluorescence efficiency, photostability, and optoelectronic properties. PDI derivatives are reported to form well-tailored supramolecular architectures: cofacial with minor slip (H-aggregates), staggered with major slip (J-aggregates), magic angle stacking (M-aggregates), rotated (X-aggregates), rotated orthogonal ((+)-aggregates), etc. H*-aggregates are defined here as an ideal case of H-aggregate with an eclipsed configuration. Although numerous reports regarding the formation and optical properties of various PDI aggregates are known, the key driving force within the PDI units guiding the self-assembly to form distinct aggregate systems remains elusive. To unravel the molecular-level mechanisms behind the self-assembly of PDI units by probing the intermolecular interactions, symmetry-adapted perturbation theory-based energy decomposition, potential energy surface scans, and non-covalent interaction index analyses were employed on PDI dimer models. Quantum theory of atoms in molecules and frontier molecular orbital analyses were implemented on the dimer models to comprehend the effect of heteroatoms and orbital interactions in stabilising the X-aggregates over the other PDI aggregate systems. Competition between the attractive and repulsive non-covalent interactions dictates a stability order of X > H > J > M > (+) > H* for the PDI aggregate system, while in the parent perylene system, the stability order was found to be X > (+) > H > M > J > H*.

Size Matters: A Computational Study of Hydrogen Absorption in Ionic Liquids

We combined both density functional theory and classical molecular dynamics simulations to investigate the molecular mechanisms governing hydrogen solvation in a total of 12 ionic liquids. Overall, the analysis of the structural properties under high temperature and pressure conditions revealed weak interactions between hydrogen and the ionic liquids, with a slight preference of this gas to be placed at the apolar domains. Interestingly, those ionic liquids comprising nitrate anions allow the accommodation of hydrogen molecules also in the polar areas. The study of the hydrogen velocity autocorrelation functions supports this observation. In addition, the structure of all of the tested ionic liquids was almost insensitive to the addition of hydrogen, so the available free volume and cavity formation are presumably the most important factors affecting solubility.

CO2 and H2 Activation on Zinc-Doped Copper Clusters

Here we systematically investigate the CO2 and H2 activation and dissociation on small Cun Zn0/+ (n=3-6) clusters using Density Functional Theory. We show that Cu6 Zn is a superatom, displaying an increased HOMO-LUMO gap and is inert towards CO2 or H2 activation or dissociation. While other neutral clusters weakly activate CO2 , the cationic clusters preferentially bind the CO2 in monodentate nonactivated way. Notably, Cu4 Zn allows for the dissociation of activated CO2 , whereas larger clusters destabilize all activated CO2 binding modes. Conversely, H2 dissociation is favored on all clusters examined, except for Cu6 Zn. Cu3 Zn+ and Cu4 Zn, favor the formation of formate through the H2 dissociation pathway rather than CO2 dissociation. These findings suggest the potential of these clusters as synthetic targets and underscore their significance in the realm of CO2 hydrogenation.

Interaction between escitalopram and ibuprofen or paracetamol: DFT and molecular docking on the drug-drug interactions

A large number of drugs are introduced each year to treat different diseases. Most of the time, patients suffer from more than one health problem which makes it necessary to take multiple drugs. When drugs are combined, the problem of drug-drug interaction becomes relevant. In this work, we studied the drug-drug interaction between escitalopram and ibuprofen or paracetamol using density functional theory and quantum theory of atoms in molecules. The results suggest that following the interactions, the activity of drugs changes according to site of interaction. Most reactive and most stable interactions would be preferable for the purpose of use. The in silico drug-likeness studies show that escitalopram and paracetamol couple is more bioavailable than escitalopram and ibuprofen couple. Moreover, in order to gain additional insights into the mentioned drugs' interactions, the drugs were docked separately and jointly against the potential targets for antidepressants and NSAIDs, namely 6HIS and 2PXX. The molecular docking results showed a potential improvement of the effectiveness of the drugs after combining by forming hydrogen bonds, hydrophobic contacts and π…π stacking.Communicated by Ramaswamy H. Sarma.

Study of protonated dimers of cytosine, cytidine, and deoxycytidine using survival yield method and quantum mechanics calculations

RATIONALE

Cytosine and its conjugates are prone to form protonated, triply-bonded dimers. Therefore, the nucleic-acid cytosine-rich sequence forms the four-stranded noncanonical secondary structure known as the intercalated motif (i-motif). This process has resulted in studies on cytosine protonated dimers. This communication focuses on the protonated dimers of cytosine and its nucleoside using the survival yield (SY) method and quantum mechanics calculations.

METHODS

To obtain the precursor ion fragmentation curve, the plot of SY against Ecomδ , the product ion spectra of the protonated dimers were obtained using a Waters/Micromass Q-TOF Premier mass spectrometer. Quantum mechanics calculations were performed using GAUSSIAN 16, and full geometry optimizations and energy calculations were performed within the density functional theory framework at B3LYP/6-31G(d,p).

RESULTS

The precursor ion fragmentation curve allowed the rating of the gas-phase stabilities of the analyzed protonated dimers. Substitution of sugar moiety at N1 cytosine atom decreased the gas-phase stabilities of the protonated dimers. The deoxycytidine dimer was found to be more stable than the cytidine dimer and cytidine-deoxycytidine dimer. Quantum chemical calculations indicated that cytosine aminohydroxy tautomer may be involved in the formation of protonated cytosine-cytosine nucleoside dimers but not in the formation of cytosine dimers.

CONCLUSIONS

The results obtained for nucleoside dimers indicated that the SY method may reflect the i-motif stabilities observed under physiological conditions. Therefore, the analysis of other protonated dimers of variously substituted cytosine-cytosine nucleoside using the SY method may be important to study the effect of cytosine substitution on the i-motif stabilities. Cytosine tautomer containing C2-OH… N(2H)-C4 moiety may be involved in the formation of protonated cytosine-cytosine nucleoside dimers.

Protomer of Imipramine Captured in Cucurbit[7]uril

Small molecules possessing multiple proton-accessible sites are important not only to many biological systems but also to host-guest chemistry; their protonation states are causal to boosting or hindering specific host-guest interactions. However, determining the protonation site is not trivial. Herein, we conduct electrospray ionization ion mobility spectrometry-mass spectrometry to imipramine, a known molecule with two protonation sites, based on the introduction of cucurbit[7]uril as a host molecule. For protonated imipramine, the proposed strategy allows clear distinction of the two protomers as host-guest complex ions and can be leveraged to capture the energetically less preferable protomer of the protonated imipramine.

Interrelations between Linkage Isomers of an Efficient Square-planar Nickel(II) Nitrite Photoswitch in the Solid State

An efficient nitrite nickel(II) photoswitch, with the 1-phenyl-2-hydroxyimino-3-[(2'-dimethylamino)ethyl]imino-1-propanone moiety used as the ancillary ligand, is reported. In the ground-state ('dark') crystal structure, the studied compound exists predominantly as the nitro-(η1 -N(O)2 ) isomer, however, traces of the exo- and endo-nitrito-(η1 -ONO) forms are detected both at 100 K (4-5 % each) and under ambient conditions (~9 % each). When excited with the 405-530 nm LED light, the nitro-to-nitrito isomerization takes place. The total conversion exceeds 90 %. The exo-nitrito linkage isomer constitutes the dominant photo-generated form, whereas the relative population of both nitrito species depends on temperature. The reaction is fully reversible and reproducible. The photo-products are stable up to 200 K. The system constitutes a good model case for the reaction mechanism studies. Thus, experimental and theoretical investigations on the photo-isomerism were conducted and are presented in detail. Eventually, the nitro→exo-nitrito→endo-nitrito reaction pathway is proposed.

Binding Properties of Small Electrophilic Anions [B6 X5 ]- and [B10 X9 ]- (X=Cl, Br, I): Activation of Small Molecules Based on π-Backbonding

Superelectrophilic anions constitute a special class of molecular anions that show strong binding of weak nucleophiles despite their negative charge. In this study, the binding characteristics of smaller gaseous electrophilic anions of the types [B6 X5 ]- and [B10 X9 ]- (with X=Cl, Br, I) were computationally and experimentally investigated and compared to those of the larger analogues [B12 X11 ]- . The positive charge of vacant boron increases from [B6 X5 ]- via [B10 X9 ]- to [B12 X11 ]- , as evidenced by increasing attachment enthalpies towards typical σ-donor molecules (noble gases, H2 O). However, this behavior is reversed for σ-donor-π-acceptor molecules. [B6 Cl5 ]- binds most strongly to N2 and CO, even more strongly than to H2 O. Energy decomposition analysis confirms that the orbital interaction is responsible for this opposite trend. The extended transition state natural orbitals for chemical valence method shows that the π-backdonation order is [B6 X5 ]- >[B10 X9 ]- >[B12 X11 ]- . This predicted order explains the experimentally observed red shifts of the CO and N2 stretching fundamentals compared to those of the unbound molecules, as measured by infrared photodissociation spectroscopy. The strongest red shift is observed for [B6 Cl5 N2 ]- : 222 cm-1 . Therefore, strong activation of unreactive σ-donor-π-acceptor molecules (commonly observed for cationic transition metal complexes) is achieved with metal-free molecular anions.

Quantum DFT studies on the drug delivery of favipiravir using pristine and functionalized chitosan nanoparticles

Considering the spread of the COVID-19 pandemic, finding new drugs along with the development of effective drug delivery methods can help in the treatment of this disease. For this reason, in this research work, the possibility of drug-delivery of Favipiravir (FP), one of the drugs approved in the treatment of COVID-19, by pristine chitosan (Chit) nanoparticles (NP), and functionalized chitosan nanoparticles with N-acylate, N-methyl, O-acetyl, and Oxazoline functional groups was studied using quantum mechanical DFT methods at B3LYP-D3(BJ)/6-311 + g(d,p) theoretical level in water medium. The QTAIM, NBO, DOS, frontier orbital, conceptual-DFT indices, and non-covalent interaction analysis were further implemented to investigate the possible interactions between FP and Chit NPs. The results show that the adsorption of FP on Chit NPs is done through the creation of hydrogen bonds, and the highest absorption energy of - 18.15 kcal/mol between pristine chitosan and FP. In the case of all functionalized Chit NPs, a decrease in the absorption energy is observed, which is more noticeable in the case of N-acylated and O-acetyl functionalize Chit NPs, and indicates the weakening of the van der Waals interactions for these cases. Considering the compatibility of Chit NPs with the human body and their non-toxicity, as well as the fact that factors such as pH, solubility, the ionic strength, and so on can be adjusted to control the release rate using the functionalized Chit NPs, it seems that the results of this work can be a comprehensive guide to design the drug delivery methods of FP drug using Chit NPs, to reduce the symptoms of COVID-19 disease.

Stability improvement of UV-filter between methoxy cinnamic acid derivatives and cyclodextrins inclusion complexes based on DFT and TD-DFT investigations

Structures and UV-vis absorption spectra of the host-guest interaction of the methoxy cinnamic acid (MCA) derivatives and cyclodextrins (CDs) were performed by using the density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations. All geometries of MCA derivatives (4-MCA, 245-MCA, 246-MCA), three types of CD (αCD, βCD, γCD), and five host-guest inclusion complexes between MCA and CD consisting of 4-MCA/αCD (1), 4-MCA/βCD (2), 245-MCA/βCD (3), 246-MCA/βCD (4), and 246-MCA/γCD (5) were fully optimized by using the M06-2X/6-31G (d,p) levels of theory. Two orientations (A and B) of the MCA guest molecule were considered. Upon examining the optimized geometry, five complexes of the methoxy cinnamic acid molecules are located inside the cavity of CD. Orientation B was more stable than orientation A because of the stronger intermolecular hydrogen bonds between the hydroxyl group of CD and the carboxylic group of MCA. The results indicated that the intermolecular hydrogen bond is mainly the driving force of formation between methoxy cinnamic acid and cyclodextrins. To reveal the host-guest interaction that is relevant to UV-filter compounds, the UV-vis absorption spectra were performed using TD-DFT calculations. The obtained results confirmed that orientation B is the most stable orientation and can absorb in both UVB and UVA regions which is similar to the parent MCA. Therefore, this knowledge will bring to understand the host-guest interaction between methoxy cinnamic acid and cyclodextrin complexes. The theoretical results are expected to provide valuable information for improving the stability of further UV-filter compounds.

Boosting Phosphoric Acid Retention in Polymer Electrolyte Membranes by Zwitterions: Insights from DFT Calculations and MD Simulations

Effective retention of phosphoric acid (PA) is crucial for the efficient operation of fuel cells based on PA-doped polymeric membranes, which is highly challenging due to the moisture-induced loss of PA. Therefore, a comprehensive understanding of the interplay among PA, functional groups, and water is essential for designing membrane materials. Using density functional theory (DFT) calculations and molecular dynamics (MD) simulations, we unveil the remarkable capability of zwitterions to effectively sequester PA, thereby unlocking the potential for fuel cell optimization. Our DFT calculations show that zwitterions, termed "charged proton-accepting bases", exhibit stronger interactions with PA compared to the traditional neutral proton-accepting bases. Furthermore, the presence of water amplifies such a discrepancy, with the zwitterion-PA interactions playing a dominant role in the zwitterion-PA-water cluster due to the strongest affinity of zwitterions to PA. Conversely, the ability of neutral bases to retain PA is significantly attenuated by moisture as the interactions between water and PA surpass those between neutral bases and PA. The strong zwitterion-PA associations arise primarily from the formation of multiple hydrogen bonds. Furthermore, MD simulations reveal the uniform distribution of zwitterions in aqueous environments and their pronounced affinities for both PA and water. In contrast, neutral bases tend to aggregate, interacting limitedly with PA. These findings underscore the effectiveness of zwitterions in boosting PA retention in fuel cells.

Toward an Accurate Black-Box Tool for the Kinetics of Gas-Phase Reactions Involving Barrier-less Elementary Steps

An enhanced computational protocol has been devised for the accurate characterization of gas-phase barrier-less reactions in the framework of the reaction-path (RP) and variable reaction coordinate variational transition-state theory. In particular, the synergistic combination of density functional theory and Monte Carlo sampling to optimize reactive fluxes led to a reliable yet effective computational workflow. A black-box strategy has been developed for selecting the most suited density functional with reference to a high-level one-dimensional reference potential. At the same time, different descriptions of hindered rotations are automatically selected, depending on the corresponding harmonic frequencies along the RP. The performance of the new tool is investigated by means of two prototypical reactions involving different degrees of static and dynamic correlation, namely, H2S + Cl and CH3 + CH3. The remarkable agreement of the computed kinetic parameters with the available experimental data confirms the accuracy and robustness of the proposed approach. Together with their intrinsic interest, these results also pave the way toward systematic investigations of gas-phase reactions involving barrier-less elementary steps by a reliable, user-friendly tool, which can be confidently used also by nonspecialists.

DFT Model of Elemental Sulfur in Sulfolane Solutions

The structure and the thermodynamic and optical (UV) properties of elemental sulfur solution in sulfolane (Sl) have been studied using density functional theory methods. The cyclic molecular form of sulfur (S8 "crown") was found using PBE1PBE/6-311+G(d,p) approximation in combination with a polarizable continuum model (the integral equation formalism variant) to exist in sulfolane medium as a Sl-S8-Sl solvate. It has been theoretically established that sulfur can form stable (S8)n clusters in concentrated solutions. An increase in the extent of association (n) of the sulfur cluster leads to a decrease in the extinction coefficient [TD-DFT(TPSSTPSS/6-311+G(d,p))] of the most intense absorption maximum lying at about 50,000 cm-1 while maintaining the shape of the remaining part of the spectrum. The observed pattern qualitatively expresses the spectral regularities of solutions with different concentrations of sulfur in sulfolane. It has been proposed that a model of the absorption spectrum of elemental sulfur suggests a minor contribution of the S12 molecular form (G298°((S12)2) - G298°((S8)3) ≈ -15.5 kJ mol-1). The findings of the study will provide deeper insights into the transformation of molecular forms of sulfur and more precisely analyze processes involving sulfur as an acting species using electronic spectroscopy.

Theoretical investigation of solvent and oxidation/deprotonation effects on the electronic structure of a mononuclear Ru-aqua-polypyridine complex in aqueous solution

Mononuclear polypyridine ruthenium (Ru) complexes can catalyze various reactions, including water splitting, and can also serve as photosensitizers in solar cells. Despite recent progress in their synthesis, accurately modeling their physicochemical properties, particularly in solution, remains challenging. Herein, we conduct a theoretical investigation of the structural and electronic properties of a mononuclear Ru-aqua polypyridine complex in aqueous solution, considering five of its possible oxidation/protonation states species: [RuII(H2O)(py)(bpy)2]2+, [RuII(OH)(py)(bpy)2]+, [RuIII(H2O)(py)(bpy)2]3+, [RuIII(OH)(py)(bpy)2]2+ and [RuIV(O)(py)(bpy)2]2+, where py = pyridine and bpy = 2,2'-bipyridine. At first, we investigate the impact of proton-coupled and non-coupled electron transfer reactions on the geometry and electronic structure of the complexes in vacuum and in solution, using an implicit solvent model. Then, using a sequential multiscale approach that combines quantum mechanics and molecular mechanics (S-QM/MM), we examine the explicit solvent effects on the electronic excitations of the complexes, and compare them with the experimental results. The complexes were synthesized, and their absorption spectra measured in aqueous solution. To accurately describe the QM interactions between the metal center and the aqueous ligand in the MM simulations, we developed new force field parameters for the Ru atom. We analyze the solvent structure around the complexes and account for its explicit influence on the polarization and electronic excitations of the complexes. Notably, accounting for the explicit solvent polarization effects of the first solvation shells is essential to correctly describe the energy of the electronic transitions, and the explicit treatment of the hydrogen bonds at the QM level in the excitation calculations improves the accuracy of the description of the metal-to-ligand charge-transfer bands. Transition density matrix analysis is used to characterize all electronic transitions in the visible and ultraviolet ranges according to their charge-transfer (CT) character. This study elucidates the electronic structure of those ruthenium polypyridyl complexes in aqueous solution and underscores the importance of precisely describing solvent effects, which can be achieved employing the S-QM/MM method.

Phase Separation and Ion Diffusion in Ionic Liquid, Organic Solvent, and Lithium Salt Electrolyte Mixtures

The highly desirable characteristics of ternary mixtures of ionic liquids, organic solvents, and metal salts make them a promising candidate for use in various electrothermal energy storage and conversion systems. In this study, using large-scale classical molecular dynamics simulations, we looked into 10 different ternary electrolyte mixtures using combinations of [EMIM]+, [BMIM]+, and [OMIM]+ cations with [NO3]-, [BF4]-, [PF6]-, [ClO4]-, [TFO]-, and [NTf2]- anions, tetraglyme, and Li salt to study the effect of ionic liquid composition on the phase behavior of ternary electrolyte mixtures. We uncovered that in these electrolytes, phase separation is mainly a function of pairwise binding energy of the constituents of the mixture. To corroborate this theory, several simulations are performed at various temperatures ranging from 260 to 500 K for each mixture, followed by calculating the binding energy of ionic liquid pairs using density functional theory. Our results verify that the transition temperature for the phase separation of each system is indeed a function of the pairwise binding energy of its ionic liquid pairs. It is also found that in some cases, the diffusion coefficient of the Li+ ions decreased even with the increase in the temperature, an effect that is attributed to the presence of condensed ionic domains in the electrolyte. This study provides a new insight for the design of multicomponent electrolyte mixtures for a wide range of energy applications.

Strong Chiroptical Effects in the Absorption and Emission of Macrocycles Based on the 2,5-Diaminoterephthalate Minimal Fluorophore

Chiral fluorescent macrocycles consisting of two to four units of dimethyl 2,5-diaminoterephthalate can be readily synthesized in a one-pot manner from inexpensive building blocks. Depending on the concentration, either a paracyclophane-like dimer with closely stacked benzene rings or a triangular trimer is the main product of the reaction. The macrocycles exhibit fluorescence in solution as well as in the solid state with maxima that are red-shifted with decreasing size of the macrocyclic ring and are observed at wavelengths from 590 (tetramer in solution) to 700 nm (dimer in the solid state). Chirality dictates the differential absorption and emission of circularly polarized light by these molecules. The ECD and CPL effects are particularly strong for the trimer, which is characterized by relatively large dissymmetry factors gabs =±2.8×10-3 at 531 nm and glum =±2.3×10-3 at 580 nm in n-hexane, being at the same time highly luminescent (Φfl =13.7 %). Despite the small chromophore, the circularly polarized brightness BCPL of 2.3 dm3  mol-1  cm-1 is comparable to values reported for other classes of established CPL emitters in the visible region, such as expanded helicenes or larger π-conjugated systems.

Investigation of the Inhibition Mechanism of Xanthine Oxidoreductase by Oxipurinol: A Computational Study

Xanthine oxidoreductase (XOR) is an enzyme found in various organisms. It converts hypoxanthine to xanthine and urate, which are crucial steps in purine elimination in humans. Elevated uric acid levels can lead to conditions like gout and hyperuricemia. Therefore, there is significant interest in developing drugs that target XOR for treating these conditions and other diseases. Oxipurinol, an analogue of xanthine, is a well-known inhibitor of XOR. Crystallographic studies have revealed that oxipurinol directly binds to the molybdenum cofactor (MoCo) in XOR. However, the precise details of the inhibition mechanism are still unclear, which would be valuable for designing more effective drugs with similar inhibitory functions. In this study, molecular dynamics and quantum mechanics/molecular mechanics calculations are employed to investigate the inhibition mechanism of XOR by oxipurinol. The study examines the structural and dynamic effects of oxipurinol on the pre-catalytic structure of the metabolite-bound system. Our results provide insights on the reaction mechanism catalyzed by the MoCo center in the active site, which aligns well with experimental findings. Furthermore, the results provide insights into the residues surrounding the active site and propose an alternative mechanism for developing alternative covalent inhibitors.

Complexes of HXeY with HX (Y, X = F, Cl, Br, I): Symmetry-Adapted Perturbation Theory Study and Anharmonic Vibrational Analysis

A comprehensive analysis of the intermolecular interaction energy and anharmonic vibrations of 41 structures of the HXeY⋯HX (X, Y = F, Cl, Br, I) family of noble-gas-compound complexes for all possible combinations of Y and X was conducted. New structures were identified, and their interaction energies were studied by means of symmetry-adapted perturbation theory, up to second-order corrections: this provided insight into the physical nature of the interaction in the complexes. The energy components were discussed, in connection to anharmonic frequency analysis. The results show that the induction and dispersion corrections were the main driving forces of the interaction, and that their relative contributions correlated with the complexation effects seen in the vibrational stretching modes of Xe-H and H-X. Reasonably clear patterns of interaction were found for different structures. Our findings corroborate previous findings with better methods, and provide new data. These results suggest that the entire group of the studied complexes can be labelled as "naturally blueshifting", except for the complexes with HI.

Effective enantioselective recognition by steady-state fluorescence spectroscopy: Towards a paradigm shift to optical sensors with unusual chemical architecture

A series of amino acid-derived 1,2,3-triazoles presenting the amino acid residue and the benzazole fluorophore connected by a triazole-4-carboxylate spacer was studied for enantioselective recognition using only steady-state fluorescence spectroscopy in solution. In this investigation, the optical sensing was performed with D-(-) and L-(+)-Arabinose and (R)-(-) and (S)-(+)-Mandelic acid as chiral analytes. The optical sensors showed specific interactions with each pair of enantiomers, allowing photophysical responses, which were used for their enantioselective recognition. DFT calculations confirm the specific interaction between the fluorophores and the analytes corroborating the observed high enantioselectivity of these compounds with the studied enantiomers. Finally, this study investigated nontrivial sensors for chiral molecules by a mechanism different than turn-on fluorescence and has the potential to broad chiral compounds with fluorophoric units as optical sensors for enantioselective sensing.

Molecular Simulation of the Interaction of Diclofenac with Halogen (F, Cl, Br)-Encapsulated Ga12As12 Nanoclusters

Diclofenac is one of the most frequently consumed over-the-counter anti-inflammatory agents globally, and several reports have confirmed its global ubiquity in several environmental compartments. Therefore, the need to develop more efficient monitoring/sensing devices with high detection limits is still needed. Herein, quantum mechanical simulations using density functional theory (DFT) computations have been utilized to evaluate the nanosensing efficacy and probe the applicability of Ga₁₂As₁₂ nanostructure and its engineered derivatives (halogen encapsulation F, Br, Cl) as efficient adsorbent/sensor materials for diclofenac. Based on the DFT computations, it was observed that diclofenac preferred to interact with the adsorbent material by assuming a flat orientation on the surface while interacting via its hydrogen atoms with the As atoms at the corner of the GaAs cage forming a polar covalent As-H bond. The adsorption energies were observed to be in the range of -17.26 to -24.79 kcal/mol and therefore suggested favorable adsorption with the surface. Nonetheless, considerable deformation was observed for the Br-encapsulated derivative, and therefore, its adsorption energy was observed to be positive. Additionally, encapsulation of the GaAs nanoclusters with halogens (F and Cl) enhanced the sensing attributes by causing a decrease in the energy gap of the nanocluster. And therefore, this suggests the feasibility of the studied materials as potentiometric sensor materials. These findings could offer some implications for the potential application of GaAs and their halogen-encapsulated derivatives for electronic technological applications.

Exploring the Microscopic Aspects of 1-Methyl-3-octylimidazolium Tetrafluoroborate Mixtures with Formamide, N-Methylformamide, and N,N-Dimethylformamide by Multiple Spectroscopic Techniques and Computations

The microscopic aspects of 1-methyl-3-octylimidazolium tetrafluoroborate ([MOIm][BF₄]) mixtures with formamide (FA), N-methylformamide (NMF), and N,N-dimethylformamide (DMF) were investigated using spectroscopic techniques of femtosecond Raman-induced Kerr effect spectroscopy (fs-RIKES), FT-IR, and NMR. Molecular dynamics simulations and quantum chemistry calculations were also performed. According to fs-RIKES, the first moment of the low-frequency spectrum bands mainly originating from the intermolecular vibrations in the [MOIm][BF₄]/FA and [MOIm][BF₄]/DMF systems changed gradually with the molecular liquid mole fraction X_ML but that in the [MOIm][BF₄]/NMF system was constant up to X_NMF = 0.7 and then gradually increased in the range of X_NMF ≥ 0.7. Excluding the contribution of the 2D hydrogen-bonding network due to the presence of FA in the low-frequency spectrum band, the X_ML dependence of the normalized first moment of the low-frequency band in the [MOIm][BF₄]/FA and [MOIm][BF₄]/NMF systems revealed that the normalized first moment did not remarkably change in the range of X_ML < 0.7 but drastically increased in X_ML ≥ 0.7. FT-IR results indicated that the amide C═O band shifted to the low-frequency side with increasing X_ML for the three mixtures due to the hydrogen bonds. The imidazolium ring C-H band also showed a similar tendency to the amide C═O band. ¹⁹F NMR probed the microenvironment of [BF₄]^- in the mixtures. The [MOIm][BF₄]/NMF and [MOIm][BF₄]/DMF systems showed an up-field shift of the F atoms of the anion with increasing X_ML, and the [MOIm][BF₄]/FA system exhibited a down-field shift. Steep changes in the chemical shifts were confirmed in the region of X_ML > 0.8. On the basis of the quantum chemistry calculations, the observed chemical shifts with increasing X_ML were mainly attributed to the many-body interactions of ions and amides for the [MOIm][BF₄]/FA and [MOIm][BF₄]/DMF systems. Meanwhile, the long distance between the cation and the anion was due to the high dielectric medium for the [MOIm][BF₄]/NMF system, which led to an up-field shift.

Dimer Rhenium Tetrafluoride with a Triple Bond Re-Re: Structure, Bond Strength

Based on the data of the gas electron diffraction/mass spectrometry (GED/MS) experiment, the composition of the vapor over rhenium tetrafluoride at T = 471 K was established, and it was found that species of the Re₂F₈ is present in the gas phase. The geometric structure of the Re₂F₈ molecule corresponding to D_4h symmetry was found, and the following geometric parameters of the r_h1 configuration were determined: r_h1(Re-Re) = 2.264(5) Å, r_h1(Re-F) = 1.846(4) Å, α(Re-Re-F) = 99.7(0.2)°, φ(F-Re-Re-F) = 2.4 (3.6)°. Calculations by the self-consistent field in full active space approximation showed that for Re₂F₈, the wave function of the ¹A_1g ground electronic state can be described by the single closed-shell determinant. For that reason, the DFT method was used for a structural study of Re₂X₈ molecules. The description of the nature of the Re-Re bond was performed in the framework of Atom in Molecules and Natural Bond Orbital analysis. The difference in the experimental values of r(Re-Re) in the free Re₂F₈ molecule and the [Re₂F₈]^2- dianion in the crystal corresponds to the concept of a triple σ²π⁴ (Re^IV-Re^IV) bond and a quadruple σ²π⁴δ² (Re^III-Re^III) bond, respectively, which are formed between rhenium atoms due to the interaction of d-atomic orbitals. The enthalpy of dissociation of the Re₂F₈ molecular form in two monomers ReF₄ (Δ_dissH°(298) = 109.9 kcal/mol) and the bond energies E(Re-Re) and E(Re-X) in the series Re₂F₈→Re₂Cl₈→Re₂Br₈ molecules were estimated. It is shown that the Re-Re bond energy weakly depends on the nature of the halogen, while the symmetry of the Re₂Br₈ (D_4d) geometric configuration differs from the symmetry of the Re₂F₈ and Re₂Cl₈ (D_4h) molecules.

Structures and stabilities of PAH clusters solvated by water aggregates: The case of the pyrene dimer

Although clusters made of polycyclic aromatic hydrocarbon and water monomers are relevant objects in both atmospheric and astrophysical science, little is known about their energetic and structural properties. In this work, we perform global explorations of the potential energy landscapes of neutral clusters made of two pyrene units and one to ten water molecules using a density-functional-based tight-binding (DFTB) potential followed by local optimizations at the density-functional theory level. We discuss the binding energies with respect to various dissociation channels. It shows that cohesion energies of the water clusters interacting with a pyrene dimer are larger than those of the pure water clusters, reaching for the largest clusters an asymptotic limit similar to that of pure water clusters and that, although the hexamer and octamer can be considered magic numbers for isolated water clusters, it is not the case anymore when they are interacting with a pyrene dimer. Ionization potentials are also computed by making use of the configuration interaction extension of DFTB, and we show that in cations, the charge is mostly carried by the pyrene molecules.

SERS-based detection of 5-S-cysteinyl-dopamine as a novel biomarker of Parkinson's disease in artificial biofluids

The early detection of Parkinson's disease (PD) can significantly improve treatment and quality of life in patients. 5-S-Cysteinyl-dopamine (CDA) is a key metabolite of high relevance for the early detection of PD. Therefore, its sensitive detection with fast and robust methods can improve its use as a biomarker. In this work we show the potentialities of label-free SERS spectroscopy in detecting CDA in aqueous solutions and artificial biofluids, with a simple, fast and sensitive approach. We present a detailed experimental SERS band assignment of CDA employing silver nanoparticle (AgNP) substrates in aqueous media, which was supported by theoretical calculations and simulated Raman and SERS spectra. The tentative orientation of CDA over the AgNP was also studied, indicating that catechol and carboxylic acid play a key role in the metallic surface adsorption. Moreover, we showed that SERS can allow us to identify CDA in aqueous media at low concentration, leading to the identification of some of its characteristic bands in pure water and in synthetic cerebrospinal fluid (SCSF) below 1 × 10^-8 M, while its band identification in simulated urine (SUR) can be reached at 1 × 10^-7 M. In conclusion, we show that CDA can be suitably detected by means of label-free SERS spectroscopy, which can significantly improve its sensitive detection for further analytical studies as a novel biomarker and further clinical diagnosis in PD patients.

Synthesis and conformational preferences of peptides and proteins with cysteine sulfonic acid

Cysteine sulfonic acid (Cys-SO₃H; cysteic acid) is an oxidative post-translational modification of cysteine, resulting from further oxidation from cysteine sulfinic acid (Cys-SO₂H). Cysteine sulfonic acid is considered an irreversible post-translational modification, which serves as a biomarker of oxidative stress that has resulted in oxidative damage to proteins. Cysteine sulfonic acid is anionic, as a sulfonate (Cys-SO₃^-; cysteate), in the ionization state that is almost exclusively present at physiological pH (pK_a ∼ -2). In order to understand protein structural changes that can occur upon oxidation to cysteine sulfonic acid, we analyzed its conformational preferences, using experimental methods, bioinformatics, and DFT-based computational analysis. Cysteine sulfonic acid was incorporated into model peptides for α-helix and polyproline II helix (PPII). Within peptides, oxidation of cysteine to the sulfonic acid proceeds rapidly and efficiently at room temperature in solution with methyltrioxorhenium (MeReO₃) and H₂O₂. Peptides containing cysteine sulfonic acid were also generated on solid phase using trityl-protected cysteine and oxidation with MeReO₃ and H₂O₂. Using methoxybenzyl (Mob)-protected cysteine, solid-phase oxidation with MeReO₃ and H₂O₂ generated the Mob sulfone precursor to Cys-SO₂^- within fully synthesized peptides. These two solid-phase methods allow the synthesis of peptides containing either Cys-SO₃^- or Cys-SO₂^- in a practical manner, with no solution-phase synthesis required. Cys-SO₃^- had low PPII propensity for PPII propagation, despite promoting a relatively compact conformation in ϕ. In contrast, in a PPII initiation model system, Cys-SO₃^- promoted PPII relative to neutral Cys, with PPII initiation similar to Cys thiolate but less than Cys-SO₂^- or Ala. In an α-helix model system, Cys-SO₃^- promoted α-helix near the N-terminus, due to favorable helix dipole interactions and favorable α-helix capping via a sulfonate-amide side chain-main chain hydrogen bond. Across all peptides, the sulfonate side chain was significantly less ordered than that of the sulfinate. Analysis of Cys-SO₃^- in the PDB revealed a very strong propensity for local (i/i or i/i + 1) side chain-main chain sulfonate-amide hydrogen bonds for Cys-SO₃^-, with >80% of Cys-SO₃^- residues exhibiting these interactions. DFT calculations conducted to explore these conformational preferences indicated that side chain-main chain hydrogen bonds of the sulfonate with the intraresidue amide and/or with the i + 1 amide were favorable. However, hydrogen bonds to water or to amides, as well as interactions with oxophilic metals, were weaker for the sulfonate than the sulfinate, due to lower charge density on the oxygens in the sulfonate.

A New Motif in Halogen Bonding: Cooperative Intermolecular S-Br⋅⋅⋅O, O⋅⋅⋅F, and F⋅⋅⋅F Associations in the Crystal Packing of α,ω-Di(sulfonyl bromide) Perfluoroalkanes

We recently reported the first examples of S-Cl⋅⋅⋅O halogen bonding complemented by short F⋅⋅⋅F contacts between neighboring chains that resulted in stabilized crystals of ClSO₂ (CF₂ )₄ SO₂ Cl and ClSO₂ (CF₂ )₆ SO₂ Cl. More recently, other researchers studied our crystallographic data further using an Independent Gradient Model (IGM), and they suggested if one goes beyond IUPAC's proposed 'less than the sum of the van der Waals radii' criterion that even more noncovalent interactions between fluorine atoms on neighboring chains as well as Cl⋅⋅⋅Cl, Cl⋅⋅⋅S, O⋅⋅⋅F, and O⋅⋅⋅S attractive interactions can be found. With that said, we have prepared samples of the related BrSO₂ (CF₂ )_n SO₂ Br derivatives (where n=4, 6, 8, and others), which give rise to even stronger S-Br⋅⋅⋅O halogen bonding interactions complemented minimally by O⋅⋅⋅F and F⋅⋅⋅F intermolecular interactions as shown by X-ray crystallography and computational chemistry using IGM isosurface plots. Additional spectroscopic characterization (multinuclear NMR, FT-IR, and MS) of the disulfonyl bromide derivatives BrSO₂ (CF₂ )₄ SO₂ Br, BrSO₂ (CF₂ )₆ SO₂ Br, and BrSO₂ (CF₂ )₈ SO₂ Br has also been obtained as well as some preliminary spectroscopic evidence for BrSO₂ (CF₂ )₂ SO₂ Br and BrSO₂ CF₂ O(CF₂ )₂ OCF₂ SO₂ Br. The implication of these results toward the preparation of the corresponding disulfonyl iodides is discussed.

Comparative study of the efficiency of silicon carbide, boron nitride and carbon nanotube to deliver cancerous drug, azacitidine: A DFT study

Herein we have made a comparative study of the efficiency of three different nanotubes viz. Carbon nanotube (CNT), boron nitride nanotube (BNNT) and silicon carbide nanotube (SiCNT) to deliver the cancerous drug, Azacitidine (AZD). The atomistic description of the encapsulation process of AZD in these nanotubes has been analyzed by evaluating parameters like adsorption energy, electrostatic potential map, reduced density gradient (RDG). Higher adsorption energy of AZD with BNNT (-0.66eV), SiCNT (-0.92eV) compared to CNT (-0.56eV) confirms stronger binding affinity of the drug for the former than the later. Charge density and electrostatic potential map suggest that charge separation involving BNNT and CNT is more prominent than SiCNT. Evaluation of different thermodynamic parameters like Gibbs free energy, enthalpy change revealed that the overall encapsulation process is spontaneous and exothermic in nature and much favorable with BNNT and SiCNT. Stabilizing interactions of the drug with BNNT and SiCNT has been confirmed from RDG analysis. ADMP molecular dynamics simulation supports that the encapsulation process of the drug within the NT at room temperature. These results open up unlimited opportunities for the applications of these NTs as a drug delivery system in the field of nanomedicine.