Spatio-temporal variations in dissolved trace elements in peat bog porewaters impacted by dust inputs from open-pit mining activities in the Athabasca Bituminous Sands (ABS) region

Considerable volumes of dust are generated from open-pit bitumen mining operations in northern Alberta, Canada. The reactive mineral phases of these dust particles can potentially dissolve in acidic (pH < 4) bog waters. Their dissolution could release trace elements (TEs), which could eventually alter these bog ecosystems. The impact of dust dissolution on the abundance of TEs in the dissolved (<0.45 μm) fraction of porewaters from excavated pits (30-40 cm deep) in the ombrogenic zone of five peatlands was evaluated. Porewaters were collected from four bogs situated within 70 km of mines and upgraders in the Athabasca Bituminous Sands (ABS) region, Alberta, Canada, and from a reference bog situated 264 km away. Over two consecutive years, the dissolved concentrations of some conservative (Al, Th, Y) and mobile lithophile elements (Fe, Li, Mn, Sr), as well as the metals enriched in bitumen (V, Ni, Mo), all increased with proximity to the mining area, in the ABS region. These trends reflect the observed increase in dust deposition with proximity to the mining area from independent studies of snow, lichens, and Sphagnum moss. Contrarily, the impact of dust dissolution on the concentration of potentially toxic TEs (As, Cd, Pb, Sb, and Tl) was negligible. Thus, the elements which are more abundant in the porewaters near industry are either ecologically benign (e.g. Li and Sr) or essential micronutrients (e.g. Fe, Mn, Ni, and Mo). Manganese was the only element which was enriched by more than 10x at all sites near the mining area, compared to its concentration at the reference site. The enrichments of all other elements were <10x, indicating that anthropogenic dust emissions from mining areas have had only a modest effect on the TEs abundance in peat porewaters.

Chemical reactivity of graphene doped with 3d transition metals: nothing compares to a single vacancy

CONTEXT

Finding catalysts that do not rely on the use of expensive metals is one of the requirements to achieve sustainable production. The reactivity of graphene doped with 3d transition metals was studied. All dopants enhanced the reactivity of graphene and performed better than Stone-Wales defects and divacancies, but were inferior to monovacancies. For hydrogenation of doped-monovacancies, Sc, Ti, Cr, Co, and Ni induced more prominent reactivity on the carbon atoms. However, the metals were the most reactive center for V, Mn, and Fe-doped graphene. Cu and Zn turned the four neighboring carbon atoms into the preferred sites for hydrogenation. The addition of oxygen to doped graphene with Ti, V, Cr, Mn, Fe, Co, and Ni on a monovacancy revealed a more uniform pattern since the metal, preferred to react with oxygen. However, Sc induced a larger reactivity on the carbon atoms. The affinity of the 3d metal-doped graphene systems towards oxygen was inferior to that observed for single-vacancies. Therefore, vacancy engineering is the most favorable and least expensive method to enhance the reactivity of graphene.

METHODS

We applied Truhlar's M06-L method accompanied by the 6-31G* basis sets to perform periodic boundary conditions calculations as implemented in Gaussian 09. The ultrafine grid was employed and the unit cells were sampled employing 100 k-points. Results were visualized employing Gaussview 5.0.1.

Time-resolved vibrational dynamics: Novel opportunities for sensing and imaging

The evolution of time-resolved spectroscopies has resulted in significant advancements across numerous scientific disciplines, particularly those concerned with molecular electronic states. However, the intricacy of molecular vibrational spectroscopies, which provide comprehensive molecular-level information within complex structures, has presented considerable challenges due to the ultrashort dephasing time. Over recent decades, an increasing focus has been placed on exploring the temporal progression of bond vibrations, thereby facilitating an improved understanding of energy redistribution within and between molecules. This review article focuses on an array of time-resolved detection methodologies, each distinguished by unique technological attributes that offer exclusive capabilities for investigating the physical phenomena propelled by molecular vibrational dynamics. In summary, time-resolved vibrational spectroscopy emerges as a potent instrument for deciphering the dynamic behavior of molecules. Its potential for driving future progress across fields as diverse as biology and materials science is substantial, marking a promising future for this innovative tool.

Deeper Defluorination and Mineralization of a Novel PFECA (C7 HFPO-TA) in Vacuum UV/Sulfite: Unique Mechanism of H/OCF3 Exchange

C7 HFPO-TA is a newly identified alternative to PFOA, which possesses a unique structure fragment (CF3O-CF(CF3)-). In this study, we evaluated the chemical reactivity of C7 HFPO-TA in advanced oxidation and reduction processes for the first time, which revealed a series of unexpected transformation mechanisms. The results showed that reductive degradation based on hydrated electrons (eaq-) was more feasible for the degradation of C7 HFPO-TA. For oxidative degradation, the branched -CF3 at the α-position carbon posed as the spatial hindrance, shielding the attack of SO4•- to -COO-. The synergistic effects of HO•/eaq- and direct photolysis led to deeper defluorination and mineralization of C7 HFPO-TA in the vacuum UV/sulfite (VUV/SF) process. We identified a unique H/OCF3 exchange that converted the CF3O-CF(CF3)- into H-CF(CF3)- directly, and the SO3•- involved mechanism of C7 HFPO-TA for the first time. We revealed the branched -CF3 connected to the same carbon next to the CF3O- group affected the C-O bond cleavage site, preferring the H/OCF3 exchange pathway. The defluorination of C7 HFPO-TA was compared with PFOA and three PFECAs in the VUV/SF process, which was highly dependent on structures. Degradation kinetics, theoretical calculations, and products' analysis provided an in-depth perspective on the degradation mechanisms and pathways of C7 HFPO-TA.

Fly ash degree of reaction in hypersaline NaCl and CaCl2 brines: Effects of calcium-based additives

The pozzolanic reaction of fly ashes with calcium-based additives can be effectively used to solidify and chemically stabilize (S&S process) highly concentrated brines inside a cementitious matrix. However, complex interactions between the fly ash, the additive, and the brine typically affect the phases formed at equilibrium, and the resulting solid capacity to successfully encapsulate the brine and its contaminants. Here, the performances of two types of fly ash (a Class C and Class F fly ash) are assessed when combined with different additives (two types of cement, or lime with and without NaAlO2), and two types of brine (NaCl or CaCl2) over a range of concentrations (0 ≤ [Cl-] ≤ 2 M). The best performing matrices - i.e., the matrices with the highest Cl-containing phases content - were identified using XRD and TGA. The experimental results were then combined with thermodynamic modeling to dissociate the contribution of the fly ash from that of the additives. All results were implemented in a machine learning model that showed good accuracy at predicting the fly ash degree of reaction, allowing for the robust prediction of extended systems performance when combined with thermodynamic modeling.

Volatile organic compounds at a roadside site in Hong Kong: Characteristics, chemical reactivity, and health risk assessment

Volatile organic compounds (VOCs) and oxygenated VOCs (OVOCs) play important roles in atmospheric chemistry and are recognized as the major pollutants in roadside microenvironments of metropolitan Hong Kong, China. In this study, the ambient VOCs and OVOCs were intensively monitored at a roadside site in Hong Kong for one month during morning and evening rush hours. The emission characterizations, as well as ozone formation potentials (OFP) and hydroxyl radical (OH) loss rates (L_OH) were determined. Results from the campaign showed that the average concentrations of detected VOCs/OVOCs ranged from 0.21 to 9.67 ppb, and higher toluene to benzene (T/B) ratio was observed during evening sections due to the variation of fuel types in vehicle fleets and mix of additional emission sources in this site. On average, OVOCs had much higher concentrations than the targeted VOC species. Acetone, formaldehyde, and acetaldehyde were the three most abundant species, while formaldehyde showed the highest contributions to both OFP (32.20 %) and L_OH (16.80 %). Furthermore, potential health hazards with inhalation exposure to formaldehyde, acetaldehyde, propionaldehyde, methyl ethyl ketone (MEK), 1,3-butadiene, toluene, benzene, and acrylonitrile were found. These results reveal that it is imperative to implement efficient control measures to reduce vehicle emissions for both primary and secondary pollutants and to protect both roadside workers and pedestrians.

Ultrasound-promoted convenient and ionic liquid [BMIM]BF4 assisted green synthesis of diversely functionalized pyrazolo quinoline core via one-pot multicomponent reaction, DFT study and pharmacological evaluation

An ultrasound-assisted green protocol for one-pot synthesis of a new series of pharmaceutically relevant pyrazolo quinoline derivatives (4a-t) were synthesized, characterized, and evaluated using DFT and biological activities. Pyrazolo quinoline derivatives (4a-t) were synthesized via a three-component tandem reaction of 1,3-dicarbonyl compound (1a-b), substituted aromatic aldehyde (2a-o), and 5-amino indazole (3a) in the presence of 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM]BF₄ ionic liquid in ethanol at ambient conditions. The main purpose of the present work is selective functionalization of pyrazolo quinoline (4a-t) core excluding another potential parallel reaction under environmentally benign reaction conditions. The present protocol shows features such as amphiphilic behavior of ionic liquid during reaction transformation, and reusability of the [BMIM]BF₄ ionic liquid under mild reaction condition. All newly derived compounds were evaluated for their in vitro anti-inflammatory and antioxidant activity. Among them, compound 4c showed encouraging antioxidant activity compared with standard antioxidant ascorbic acid, and compounds 4n and 4r displayed very good anti-inflammatory activity compared with a standard drug. In this study, a theoretical computational density functional study was also executed to perform the geometry optimizations, frontier molecular orbital approach, and molecular electrostatic potential (MESP). The DFT study was carried out with the basis set DFT/B3LYP/6-31+G (d, p) level of theory. The quantum chemical descriptors (QCDS) and MESP diagrams were plotted to examine the biological reactivities of representative pyrazolo quinolines (4a-t).

Autoxidized citronellol: Free radicals as potential sparkles to ignite the fragrance induced skin sensitizing pathway

Citronellol, one of the most used fragrance compounds worldwide, is one ingredient of Fragrance Mix II used to assess skin allergy to fragrances in dermatitis patients. Pure citronellol is non-allergenic. Main issue is it autoxidizes when exposed to air becoming then allergenic. The increased skin sensitizing potency of air-exposed citronellol has been attributed to the hydroperoxides detected at high concentrations in the oxidation mixtures. It has been postulated that such hydroperoxides can give rise to specific antigens, although chemical mechanisms involved and the pathogenesis are far from being unraveled. Hydroperoxides are believed to react with skin proteins through mechanisms involving radical intermediates. Here, insights on the potential radicals involved in skin sensitization to citronellol hydroperoxides are given. The employed tool is a multispectroscopic approach based on (i) electron paramagnetic resonance and spin trapping, that confirmed the formation of oxygen- and carbon-radicals when exposing reconstructed human epidermis to concentrations of hydroperoxides close to those used for patch testing patients with air-oxidized citronellol; (ii) liquid chromatography-mass spectrometry, that proved the reaction with amino acids such as cysteine and histidine, known to be involved in radical processes and (iii) density functional theory calculations, that gave an overview on the preferential paths for radical degradation.

Revisiting the trapping of noble gases (He-Kr) by the triatomic H3+ and Li3+ species: a density functional reactivity theory study

Small atomic clusters with exotic stability, bonding, aromaticity, and reactivity properties can be made use of for various purposes. In this work, we revisit the trapping of noble gas atoms (He-Kr) by the triatomic H₃⁺ and Li₃⁺ species by using some analytical tools from density functional theory, conceptual density functional theory, and the information-theoretic approach. Our results showcase that though similar in geometry, H₃⁺ and Li₃⁺ exhibit markedly different behavior in bonding, aromaticity, and reactivity properties after the addition of noble gas atoms. Moreover, the exchange-correlation interaction and steric effect are key energy components in stabilizing the clusters. This study also finds that the origin of the molecular stability of these species is due to the spatial delocalization of the electron density distribution. Our work provides an additional arsenal towards a better understanding of small atomic clusters capturing noble gases.

Revisiting the hydroxylation phenomenon of SiO2: a study through "hard-hard" and "soft-soft" interactions

Surface hydroxylation has been extensively studied over the years for a variety of applications, and studies involving hydroxylation of different silica surfaces are still carried out due to the interesting properties obtained from those modified surfaces. Although a number of theoretical studies have been employed to evaluate details on the hydroxylation phenomenon on silica (SiO₂) surfaces, most of these studies are based on computationally expensive models commonly based on extended systems. In order to circumvent such an aspect, here we present a low-cost theoretical study on the SiO₂ hydroxylation process aiming to evaluate aspects associated with water-SiO₂ interaction. Details about local reactivity, chemical softness, and electrostatic potential were evaluated for SiO₂ model substrates in the framework of the density functional theory (DFT) using a molecular approach. The obtained results from this new and promising approach were validated and complemented by fully atomistic reactive molecular dynamics (FARMD) simulations. Furthermore, the implemented approach proves to be a powerful tool that is not restricted to the study of hydroxylation, opening a promising route for low computational cost to analyze passivation and anchoring processes on a variety of oxide surfaces.

Overlooked environmental risks deriving from aqueous transformation of bisphenol alternatives: Integration of chemical and toxicological insights

Owing to the widespread prevalence and ecotoxicity of bisphenol alternatives such as bisphenol S, bisphenol F, and bisphenol AF, the past decade has witnessed the publication of a remarkable number of studies related to their transformation and remediation in natural waters. However, the reactivity, removal efficiency, transformation products (TPs), and mechanisms of such emerging pollutants by different treatment processes have not been well elucidated. Particularly, the transformation-driven environmental risks have been mostly overlooked. Therefore, we present a review to address these issues from chemical and toxicological viewpoints. Four degradation systems can be largely classified as catalytic persulfate (PS) oxidation, non-catalytic oxidation, photolysis and photocatalysis, and biodegradation. It was found that bisphenol alternatives possess distinct reactivities with different oxidizing species, with the highest performance for hydroxyl radicals. All systems exhibit superior elimination efficiency for these compounds. The inadequate mineralization suggests the formation of recalcitrant TPs, from which the overall reaction pathways are proposed. The combined experimental and in silico analysis indicates that many TPs have developmental toxicity, endocrine-disrupting effects, and genotoxicity. Notably, catalytic PS systems and non-catalytic oxidation result in the formation of coupling products as well as halogenated TPs with higher acute and chronic toxicity and lower biodegradability than the parent compounds. In contrast, photolysis and photocatalysis generate hydroxylated and bond-cleavage TPs with less toxicity. Overall, this review highlights the secondary environmental risks from the transformation of bisphenol alternatives by conventional and emerging treatment processes. Finally, future perspectives are recommended to address the knowledge gaps of these contaminants in aquatic ecosystems.

Tower-based measurements of NMHCs and OVOCs in the Pearl River Delta: Vertical distribution, source analysis and chemical reactivity

Measurements of vertical distribution of volatile organic compounds (VOCs) have attracted wide attentions, which could help to understand atmospheric oxidation mechanism and provide implications for VOC control. This study measured the non-methane hydrocarbons (NMHCs) and oxygenated VOCs (OVOCs) simultaneously for the first time at three different heights, namely ground, 118 m and 488 m, in the Canton Tower located in the urban core of the Pearl River Delta (PRD). The results show that NMHCs decreased while some OVOC species such as formaldehyde and acetaldehyde increased with increasing height. It was mainly attributed to the dilution and chemical loss of NMHCs but secondary production of OVOCs during vertical transport. Ratio analysis and receptor modeling indicate that vehicle exhausts (47%) and fuel evaporation (39%) were major sources of the total NMHCs. Interestingly, industry contributed much more at 118 m, probably affected by organic gas discharge from the high chimney of industrial factories. The chemical reactivities in terms of OH radical loss rate (L_OH), ozone formation potential (OFP) and secondary organic aerosol potential (SOAP) were lowest at 118 m, smaller than those influenced by high fresh NMHC emissions at ground and strong formation of secondary species (e.g. OVOCs) at 488 m. OH exposure estimated by isoprene and m,p-xylene/ethylbenzene was different depending on their time scale of vertical turbulent mixing and chemical loss. OVOC species measured at different heights were positively correlated with O_x (R = 0.48-0.87), indicating that OVOCs were largely contributed by secondary formation in photochemical process. The tower measurements of NMHCs and OVOCs provided a unique opportunity to investigate the VOC distribution and chemical behaviors, which could give important information for understanding O₃ and PM_2.5 pollution mechanism in the PRD region with fast developing urban setting and substantially changing air quality.

Rényi's divergence as a chemical similarity criterion

In this work, a new version of Rényi's divergence is presented. The expression obtained is used as a tool to identify molecules that could share some chemical or structural properties, and a data basis set of 1641 molecules is used in this study. Our results suggest that this new form of Rényi divergence could be a useful tool that will eventually permit complementary studies in which the main goal is to obtain molecules with similar properties.

Heating events drive the seasonal patterns of volatile organic compounds in a typical semi-arid city

The emission characteristics, source apportionment and chemical behavior of volatile organic compounds (VOCs) are important for strategy-making on ozone (O₃) and fine particulate matter (PM_2.5) control. Based on the continuous observation during four seasons, the seasonal characteristics, chemical reactivity and source apportionment of 116 VOCs species were studied in a typical semi-arid city with no relevant research. The results showed that the annual average concentrations of total volatile organic compounds (TVOCs) in Hohhot was 44.67 ± 46.59 ppbv with the predominant of alkanes and oxygenated volatile organic compounds (OVOCs). The sharp increment of TVOCs were explained by the elevating OVOCs and alkanes in autumn, while alkanes and alkenes in winter. The levels of alkenes presented negative and positive correlations with solar radiation and PM₁₀, respectively. The mixing ratios accounted for 30% (alkanes) and 23% (alkenes and aromatics) of the TVOCs, respectively; while their ozone formation potential (OFP) ~15% and nearly 50% (even 75% in winter), respectively, indicating that the OFP of different VOCs species depends not only on their concentrations but more importantly on their chemical activity in atmosphere. According to the seasonal source apportionment, both the high levels of short-chain alkanes, alkenes and aromatics and the increasing coal sales volume suggested that the combustion sources were the predominant in heating seasons, while solvent uses was extracted as the most predominant during non-heating seasons. In non-heating seasons, the biogenic emission sources, ranking as the second contributor, were significantly higher than heating seasons. Isoprene was the most active biogenic VOCs species, bagging test results showed that deciduous trees were the predominant contributors for isoprene (~99%), while coniferous trees and shrub for monoterpenes (>95%). It will be helpful for understanding the characteristics of VOCs in Chinese national key development areas and informing policy to control semi-arid regional VOCs air pollution.

Molecular structure and quantum descriptors of cefradine by using vibrational spectroscopy (IR and Raman), NBO, AIM, chemical reactivity and molecular docking

This study aims to investigate the structural and vibrational features of cefradine (the first-generation cephalosporin antibiotic) based on spectroscopic experiments and theoretical quantum chemical approach. The fundamental structural aspects of cefradine have been examined based on optimized geometry, spectroscopic behavior, intermolecular interaction, chemical reactivity, intramolecular hydrogen bonding, and molecular docking analysis. The most stable minimum energy conformer of the title molecule was identified by performing a one-dimensional potential energy surface scan along the rotational bonds at B3LYP/6-311++G (d,p) level of theory. The vibrational features of the molecule and information about the coupled modes were predicted. The chemical reactivity and stability of all the possible conformers of cefradine were estimated based on the HOMO-LUMO energy gap and NBO approach. The overall picture of accumulation of charges on individual atoms of the molecule was predicted by molecular electrostatic potential (MEP) surface map which in turn identifies the nucleophilic and electrophilic region or sites. The quantitative analysis of electrophilicity and nucleophilicity indices was done by Hirshfeld charge analysis and it was found that N8 atom is the most prominent site for nucleophilic attack while C14 atom is feasible for electrophilic attack. QTAIM study has also been performed to investigate the nature and strength of hydrogen bonding interactions. Besides, molecular docking studies were performed to examine the active binding residues of the target.

Temperature dependence of source profiles for volatile organic compounds from typical volatile emission sources

Source profiles of volatile organic compounds (VOCs) emitted from the evaporation of various fuels, industrial raw materials, processes and products are still limited in China. The impact of ambient temperature on the VOC released from these fugitive emission sources has also been rarely reported. In order to establish VOC source profiles for thirteen volatile emission sources, a sampling campaign was conducted in Central China, and five types of sources were investigated both in winter and summer. The dominant VOC groups varied in different sources, and they were alkanes (78.6%), alkenes (53.1%), aromatics (55.1%), halohydrocarbons (80.7%) and oxygenated VOCs (OVOCs) (76.0%), respectively. Ambient temperature showed different impacts on VOC source profiles and specific species ratios. The mass percentages of halohydrocarbons emitted from color printing and waste transfer station in summer were 42 times and 20 times higher than those in winter, respectively. The mass percentages of OVOCs emitted from car painting, waste transfer station and laundry emission sources were much higher in summer (7.9-27.8%) than those in winter (0.8-2.6%). On the contrary, alkanes from color printing, car painting and waste transfer stations were about 11, 4 and 5 times higher in winter than those in summer, respectively. The coefficient of divergence values for the source profiles obtained in winter and summer ranged in 0.3-0.7, indicating obvious differences of source profiles. Benzene/toluene ratio varied in 0.00-0.76, and it was in the range of 0.02-0.50 in winter and 0.04-0.52 in summer for the same sources, respectively. Hexanal, isobutene, m,p-xylene, toluene, 2-methylacrolein, styrene, 1-hexane and cis-2-butene dominated the ozone formation potentials (OFP). The OFP summer/winter differences were 5-320 times by MIR method and 1-79 times by Propy-Equiv method, respectively. This study firstly gave direct evidence that ambient temperature modified the mass percentages of VOC species obviously. It is important for improving VOC source apportionment and chemical reactivity simulation.

Towards a converged strategy for including microsolvation in reaction mechanism calculations

A major part of chemical conversions is carried out in the fluid phase, where an accurate modeling of the involved reactions requires to also take into account solvation effects. Implicit solvation models often cover these effects with sufficient accuracy but can fail drastically when specific solvent-solute interactions are important. In those cases, microsolvation, i.e., the explicit inclusion of one or more solvent molecules, is a commonly used strategy. Nevertheless, microsolvation also introduces new challenges-a consistent workflow as well as strategies how to systematically improve prediction performance are not evident. For the COSMO and COSMO-RS solvation models, this work proposes a simple protocol to decide if microsolvation is needed and how the corresponding molecular model has to look like. To demonstrate the improved accuracy of the approach, specific application examples are presented and discussed, i.e., the computation of aqueous pK_a values and a mechanistic study of the methanol mediated Morita-Baylis-Hillman reaction.

Crystal structure, chemical reactivity, kinetic and thermodynamic studies of new ligand derived from 4-hydroxycoumarin: Interaction with SARS-CoV-2

Currently, Covid-19 pandemic infects staggering number of people around the globe and causes a high rate of mortality. In order to fight this disease, a new coumarin derivative ligand (4-[(pyridin-3-ylmethyl) amino]-2H-chromen-2-one) (LTA) has been synthesized and characterized by single-crystal X-ray diffraction, NMR, ATR, UV-Visible and cyclic voltammetry. Chemical reactivity, kinetic and thermodynamic studies were investigated using DFT method. The possible binding mode between LTA and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation. Single crystal X-ray diffraction showed that LTA crystallizes in a monoclinic system with P2 1  space group. The reactivity descriptors such as nucleophilic index confirm that LTA is more nucleophile, inducing complexation with binding species like biomolecules. The kinetic and thermodynamic parameters showed that the mechanism of crystal formation is moderately exothermic. The binding energy of the SARS-CoV-2/Mpro-LTA complex and the calculated inhibition constant using docking simulation showed that the active LTA molecule has the ability to inhibit SARS-CoV-2.

Chemical reactivity and bioactivity properties of pyrazinamide analogs of acetylsalicylic acid and salicylic acid using conceptual density functional theory

Conventional drugs used to treat Tuberculosis (TB) are becoming ineffective due to the occurrence of multiple drug resistant strains of tuberculosis (TB). This has made the TB disease a a serious global health dilemma. Hence, there is desperate necessity for the advancement of new drugs. In this work, the chemical reactivity and bioactivity of several analogs ofpyrazinamide (PZA) were investigated. PZA is one of the first-line of drugs used to treat tuberculosis and is a key contributor to shortening the treatment time for the disease. Chemical reactivity descriptors of pyrazinamide (PZA) and its analogs of acetylsalicyclic acid and salicyclic acid were investigated using conceptual density functional theory in water as a solvent at the MN12SX/Def2TZVP level of theory. Results have shown that all PZA analogs have improved their global and local reactivity indeces as compared to pyrazinamide based on its electronegativity, electrodonating power, electroaccepting power, eletrophilicity, global hardness and dual descriptor condensed fukui indexes. Moreover, their pKa values are slightly higher than PZA. In terms of its drug-likeness, all PZA analogs passed the Lipinski's Rule of Five criteria. Furthermore, their bioactivity scores are significantly better than pyrazinamide indicating good reaction to G-Protein Coupled Receptor (GPCR) ligands, kinase inhibitors, ion channel modulators, nuclear receptor ligands, protease inhibitors and other enzyme targets. Overall, the PZA analogs are found to be promising anti-tuberculosis drugs. Based on global and local reactivity descriptors, pKa and bioactivity scores, PZA analog of 5-n-Octanoylsalicylic acid is the most reactive among the PZA analogs tested.

Derivatives of pyridine and thiazole hybrid: Synthesis, DFT, biological evaluation via antimicrobial and DNA cleavage activity

A novel series of the 2-pyridine substituted 3a-e and 4-pyridine substituted 4a-e thiazole derivatives were synthesized, characterized, and evaluated for the biological activity. Crystallographic parameters and inter- and intramolecular interactions of 3a and 3c single crystals were examined through XRD analysis. The chemical reactivity potentials of the compounds were evaluated, by comparing with a theoretical approach based on DFT. The biological activity properties of synthesized compounds were determined by antimicrobial activity with Gram positive, Gram negative, Yeast via minimal inhibitory concentration (MIC) method and DNA cleavage activity studies. The most obvious findings to emerge from this study are that on the basis of both biological activity and chemical reactivity 4-pyridine thiazole hybrid compounds 4a-e showed more potent activity than 3a-e. In general, the antimicrobial activity of synthesized compounds follows the Bacillus cereus > Staphylococcus aureus > Candida albicans > Escherichia coli > Pseudomonas aeruginosa. The most potent compound 4c (MIC values 0.02 mM) exhibited antimicrobial activity against Staphylococcus aureus and Bacillus cereus. Furthermore, this compound has a good electrophilicity index value (4.56 eV).

Nitrofurantoin-melamine monohydrate (cocrystal hydrate): Probing the role of H-bonding on the structure and properties using quantum chemical calculations and vibrational spectroscopy

Cocrystal monohydrate of nitrofurantoin (NF) with melamine (MELA) has been studied as NF is an antibacterial drug used for the treatment of urinary tract infections. The structure of nitrofurantoin-melamine-monohydrate (NF-MELA-H₂O) is characterized by FT-IR and FT-Raman spectroscopy. The energies and vibrational frequencies of the optimized structures calculated using quantum chemical calculations. Supported by normal coordinate analyses and potential energy distributions (PEDs), the complete vibrational assignments recommended for the observed fundamentals of cocrystal hydrate. With the aim of inclusion of all the H-bond interactions, dimer of NF-MELA-H₂O has been studied as only two molecules of cocrystal hydrate are present in the unit cell. By the study of dimeric model consistent assignment of the FT-IR and FT-Raman spectrum obtained. H-bonds are of essential importance in an extensive range of molecular sciences. The vibrational analyses depict existence of H-bonding (O-H⋯N) between water O-H and pyridyl N atom of MELA in both monomer and dimer. To probe the strength and nature of H-bonding in monomer and dimer, topological parameters such as electron density (ρ_BCP), Laplacian of electron density (∇²ρ_BCP), total electron energy density (H_BCP) and H-bond energy (E_HB) at bond critical points (BCP) are evaluated by quantum theory of atoms in molecules (QTAIM). Natural bond orbitals (NBOs) analyses are carried out to study especially the intra and intermolecular H-bonding and their second order stabilization energy (E⁽²⁾). The value of HOMO-LUMO energy band gap for NF-MELA-H₂O (monomer and dimer both) is less than NF, showing more chemical reactivity for NF-MELA-H₂O. Chemical reactivity has been described with the assistance of electronic descriptors. Global electrophilicity index (ω = 7.3992 eV) shows that NF-MELA-H₂O behaves as a strong electrophile than NF. The local reactivity descriptors analyses such as Fukui functions, local softnesses and electrophilicity indices performed to determine the reactive sites within NF-MELA-H₂O. In MEP map of NF-MELA (monomer and dimer) electronegative regions are about NO₂ and C=O group of NF, although the electropositive regions are around NH₂, N-H group and H₂O molecule. Molar refractivity (MR) value of NF-MELA-H₂O (monomer and dimer) lies within the range set by Lipinski's modified rules. This study could set as an example to study the H-bond interactions in pharmaceutical cocrystals.

Study of molecular structure and hydrogen bond interactions in dipfluzine-benzoic acid (DIP-BEN) cocrystal using spectroscopic and quantum chemical method

The purpose of this article is to predict the molecular structure of the cocrystal of dipfluzine-benzoic acid (DIP-BEN) through computational approach (DFT calculations) and validate it using vibrational spectroscopic studies. The molecular structure of the DIP-BEN cocrystal has been predicted by forming models on the basis of the active sites available to form H-bonds between dipfluzine (DIP) and benzoic acid (BEN). Conformational study has been performed and potential energy surface scans are plotted around the flexible bonds of the cocrystal molecule and three stable conformers have been obtained. Quantum theory of atoms in molecules (QTAIM) explains that all the interactions are medium and partially covalent in nature. Natural bond orbital analysis of the second order perturbation theory of the Fock matrix suggests that interactions LP (2) O2 → σ*(O74H75) and LP (2) F1 → σ* (O89H90) are responsible for the stabilization of the molecule. The HOMO and LUMO energies and electronic charge transfer (ECT) confirms that charge flows from BEN to DIP. Global reactivity descriptor parameters suggest that DIP-BEN cocrystal is softer, thus more reactive in comparison to DIP. Local reactivity descriptor parameter is used to predict reactive sites of the cocrystal. The experimental and theoretical results support the formation of cocrystal through strong hydrogen bond (O89H90⋯F1 and O74H75⋯O2) interactions present in cocrystal.

Theoretical modelling of the chemical reactivity of fresh biomass chars under non-catalytic conditions

This study developed a model for the chemical reactivity of fresh biomass chars, and built a calculation equation for the char gasification rate using simple gas-solid collision theory (SCT). The effects of pore breaks, pore collapse and thermal annealing on the char reactivity were considered in the modelling. Experimental tests for six acid-washed biomass chars were performed under a CO₂ atmosphere and used a thermo-gravimetric analyzer (TGA) over the temperature range of 1073-1273 K. The results showed that the reactivity of fresh char could be predicted quantitatively by some characteristic properties of certain kind of biomass and their combined parameters. For the instability of the biomass char structure, the internal pore length and gasification temperature showed a good exponential relationship. Good agreement was achieved, and the applicability of the model was demonstrated by comparing the predicted results with experimental data.

Combined spectroscopic and quantum chemical approach to study the effect of hydrogen bonding interactions in ezetimibe

Molecular structure, chemical and physical reactivity, spectroscopic behavior, intermolecular interactions play an important role in understanding the biological nature of pharmaceutical drugs. The objective of the study is to combine the spectroscopic and computational methodology for the investigation of structural behavior of ezetimibe (EZT). Computational study was done on monomeric, dimeric and trimeric models of EZT using B3LYP/6-311G(d,p). Hydrogen bond interactions were taken into consideration to validate the theoretical results with the experimental one. Results obtained for trimeric model were better than monomer and dimer. HOMO-LUMO energy band gap shows that the chemical reactivity calculated using dimeric and trimeric model is higher than that of monomeric model. Higher value of electrophilicity index (ω = 2.5654 eV) also confirms that trimer behaves as a strong electrophile in comparison with monomer and dimer. To examine the hyperconjugation interactions and the stability of the molecule, natural bond analysis (NBO) was done on dimer and trimer of EZT. Nature and the strength of hydrogen bonds were examined by quantum theory of atoms in molecules (QTAIM). Binding energy calculated from counterpoise method was -7.40 kcal/mol for dimer and -21.47 kcal/mol for trimer.

Spectroscopic and molecular structure (monomeric and dimeric model) investigation of Febuxostat: A combined experimental and theoretical study

Febuxostat (FXT) is a urate-lowering drug and xanthine oxidase inhibitor which is used for the treatment of hyperuricemia and gout caused by increased levels of uric acid in the blood (hyperuricemia). The present study aims to provide deeper knowledge of the structural, vibrational spectroscopic and physiochemical properties of FXT based on monomeric and dimeric model with the aid of combination of experimental and computational methods. The conformational analysis of form Q has been done to predict the possible structure of unknown form A. Vibrational spectra of form A and Q has been compared to get an idea of hydrogen bonding interactions of form A. A computational study of FXT has been executed at different level (B3LYP, M06-2X, WB97XD) of theory and 6-31 G (d, p) basis set for dimeric model to elucidate the nature of intermolecular hydrogen bond. The red shift observed in the stretching modes of OH, CO groups and blue shift in stretching mode of CN group in experimental as well as in theoretical spectra explains the involvement of these groups in intermolecular hydrogen bonding. NBO analysis shows that change in electron density (ED) in the lone pair orbital to σ* antibonding orbital (LP1 (N39) → σ* (O3-H38)) with maximum value of E(2) energy confirms the presence of hydrogen bond (N39⋯H38-O3) leading to dimer formation. Study of topological parameters was executed for dimer using Bader's atoms in molecules (AIM) theory predicting the partially covalent nature of hydrogen bonds present in the molecule. The study of molecular electrostatic potential surface (MEPS) map ascertains that the CO, CN group are prone to electrophilic attack and OH group is active towards nucleophilic attack. The lower energy band gap and higher value of softness of dimeric model of FXT indicates its more reactivity, polarisability than monomeric model. The local reactivity descriptors predict the order of reactive sites towards electrophilic, nucleophilic and radical attack. An investigation made to determine the ligand protein interaction of FXT through docking with different molecular targets reveals the inhibitive as well as antibacterial nature of FXT.

Local electrophilicity

In this work some possibilities for deriving a local electrophilicity are studied. First, we consider the original definition proposed by Chattaraj, Maiti, and Sarkar (J Phys Chem A 107:4973, 2003), in which the local electrophilicity is given by the product of the global electrophilicity, and the Fukui function for charge acceptance is derived by two different approaches, making use of the chain rule for functional derivatives. We also modify the proposals based on the electron density so as to have a definition with the same units of the original definition, which also introduces a dependence in the Fukui function for charge donation. Additionally, we also explore other possibilities using the tools of information theory and the temperature dependent reactivity indices of the density functional theory of chemical reactivity. The poor results obtained from the last two approaches lead us to conjecture that this is due to the fact that the global electrophilicity is not a derivative, like most of the other reactivity indices. The conclusion is that Chattaraj's suggestion seems to be the simplest, but at the same time a very reliable approach to this important property.

Chemical reactivity of the frustrated Lewis pairs in borophosphines: a theoretical analysis of their Lewis acidity, Lewis basicity and Fukui function

The chemical reactivity of a set of borophosphines of the general formula R₂B-G-PY₂, where G is the connector group between the Lewis acidic site, a borane group, and the Lewis basic site, a phosphine fragment, is theoretically investigated through their Lewis acidity and Lewis basicity, as well as the location of the Fukui function and the shape of the molecular electrostatic potential. The role of some global reactivity descriptors, like the vertical ionization potential, I, and the vertical electron affinity, A, is also analyzed in order to gain a deeper insight on the intrinsic chemical reactivity of these borophosphines. We also use the energies involved in the formation of the adducts between the borophosphine and the ions H^- and H⁺ to estimate the Lewis acidity and Lewis basicity, respectively; by their nature, these energies represent local reactivity descriptors. Some of these borophosphines are able to activate the covalent bond in the hydrogen molecule. Possible paths for the hydrogen release reaction from the zwitterion R[Formula: see text]HB-G-PH[Formula: see text] are studied using the mentioned quantities, suggesting that an intramolecular hydride shift mechanism seems to be more favorable than a proton migration process. The acceptor Fukui function f⁺(r) proved to be useful to identify the acidic molecular sites for the interaction with the hydride ion and the relative stability of the corresponding adducts is related to the relative values of this function.

Electronic and optical properties of C24, C12X6Y6, and X12Y12 (X = B, Al and Y = N, P)

Utilizing first-principles calculations, we studied the electronic and optical properties of C₂₄, C₁₂X₆Y₆, and X₁₂Y₁₂ fullerenes (X = B, Al; Y = N, P). These fullerenes are energetically stable, as demonstrated by their negative cohesive energies. The energy gap of C₂₄ may be tuned by doping, and the B₁₂N₁₂ fullerene was found to have the largest energy gap. All of the fullerenes had finite optical gaps, suggesting that they are optical semiconductors, and they strongly absorb UV radiation, so they could be used in UV light protection devices. They could also be used in solar cells and LEDs due to their low reflectivities. Graphical abstract Possible applications of doped C₂₄ fullerene.

Blue M2: an intermediate melanoidin studied via conceptual DFT

In this computational study, ten density functionals, viz. CAM-B3LYP, LC-ω PBE, M11, M11L, MN12L, MN12SX, N12, N12SX, ω B97X, and ω B97XD, related to the Def2TZVP basis sets, are assessed together with the SMD solvation model for calculation of the molecular properties and structure of blue-M2 intermediate melanoidin pigment. All the chemical reactivity descriptors for the system are calculated via conceptual density functional theory (DFT). The active sites suitable for nucleophilic, electrophilic, and radical attacks are selected by linking them with the Fukui function indices, electrophilic Parr functions, and condensed dual descriptors Δf(r), respectively. The prediction of the maximum absorption wavelength is considerably accurate relative to its experimental value. The study reveals that the MN12SX and N12SX density functionals are the most appropriate density functionals for predicting the chemical reactivity of the molecule under study.

Synthesis, structure and toxicity evaluation of ethanolamine nitro/chloronitrobenzoates: a combined experimental and theoretical study

BACKGROUND

Nitroaromatic and chloronitroaromatic compounds have been a subject of great interest in industry and recently in medical-pharmaceutic field. 2-Chloro-4-nitro/2-chloro-5-nitrobenzoic acids and 4-nitrobenzoic acid are promising new agents for the treatment of main infectious killing diseases in the world: immunodeficiency diseases and tuberculosis.

RESULTS

New ethanolamine nitro/chloronitrobenzoates were synthesized and characterized by X-ray crystallography, UV-vis, FT-IR and elementary analysis techniques. The toxicity of the compounds prepared and correspondent components was evaluated using Hydractinia echinata as test system. A significant lower toxicity was observed for nitro-derivative compared with chloronitro-derivatives and individual components. Crystallographic studies, together with the chemical reactivity and stability profiles resulted from density functional theory and ab initio molecular orbital calculations, explain the particular behavior of ethanolamine 4-nitrobenzoate in biological test.

CONCLUSIONS

The experimental and theoretical data reveal the potential of these compounds to contribute to the design of new active pharmaceutical ingredients with lower toxicity.

Tautomeric transformation of temozolomide, their proton affinities and chemical reactivities: A theoretical approach

The gas-phase geometry optimizations of bare, mono- and dihydrated complexes of temozolomide isomers were carried out using density functional calculation at the M06-2X/6-31+G(d,p) level of the theory. The structures and protonation energies of protonated species of temozolomide are reported. Chemical indices of all isomers and protonated species are also reported. Energies, thermodynamic quantities, rate constants and equilibrium constants of tautomeric and rotameric transformations of all isomers I1↔TZM↔HIa↔HIb↔I2↔I3 in bare and hydrated systems were obtained.

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules

Background

Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites.

Results

This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form.

Conclusions

Due to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at http://ncbr.muni.cz/ACC.

Electronic supplementary material

The online version of this article (doi:10.1186/s13321-015-0099-x) contains supplementary material, which is available to authorized users.

Vibrational spectra, HOMO, LUMO, MESP surfaces and reactivity descriptors of amylamine and its isomers: A DFT study

Amylamine constitutes an important class of organic compounds which exists in a variety of ammonia derivatives. In present study, a comparative analysis of amylamine and its two potential isomers, iso-amylamine and tert-amylamine, has been performed using density functional theory with B3LYP method and 6-311G(d,p) as the basis set. The equilibrium structures of amylamine as well as its iso and tert forms have been obtained. The vibrational spectroscopic analysis has been carried out for the three molecules and complete assignments to all possible modes have been offered. The HOMO, LUMO and MESP surfaces are analyzed to discuss the chemical reactivity patterns in the molecules. A number of reactivity parameters have been calculated to further explain their chemical reactivity. The thermodynamic and nonlinear optical parameters are also calculated and discussed.

Molecular structure, IR spectra, and chemical reactivity of cisplatin and transplatin: DFT studies, basis set effect and solvent effect

Three different density functional theory (DFT) methods were employed to study the molecular structures of cis-diamminedichloroplatinum(II) (CDDP) and trans-diamminedichloroplatinum(II) (TDDP). The basis set effect on the structure was also investigated. By comparing the optimized structures with the experimental data, a relatively more accurate method was chosen for further study of the IR spectra and other properties as well as the solvent effect. Nineteen characteristic vibrational bands of the title compounds were assigned and compared with available experimental data. The number of characteristic peaks for the asymmetric stretching and deformation vibrations of N-H can serve as a judgment for the isomer between CDDP and TDDP. Significant solvent effect was observed on the molecular structures and IR spectra. The reduced density gradient analysis was performed to study the intramolecular interactions of CDDP and TDDP, and the nature of changes in the structures caused by the solvent was illustrated. Several descriptors determined from the energies of frontier molecular orbitals (HOMO and LUMO) were applied to describe the chemical reactivity of the title compounds. The molecular electrostatic potential (MESP) surfaces showed that the amino groups were the most favorable sites that nucleophilic reagents tend to attack, and CDDP was easier to be attacked by nucleophilic reagents than TDDP.

Integrated testing and assessment approaches for skin sensitization: a commentary

A Bayesian integrated testing strategy (ITS) approach, aiming to assess skin sensitization potency, has been presented, in which data from various types of in vitro assays are integrated and assessed in combination for their ability to predict in vivo skin sensitization data. Here we discuss this approach and compare it to our quantitative mechanistic modeling (QMM) approach based on physical organic chemistry. The main findings of the Bayesian study are consistent with our chemistry-based approach and our previously published assessment of the key determinants of sensitization potency, in particular the relatively high predictive value found for chemical reactivity data and the relatively low predictive value for bioavailability parameters. As it stands at present the Bayesian approach does not utilize the full range of predictive capability that is already available, and aims only to assign potency categories rather than numerical potency values per se. In contrast, for many chemicals the QMM approach can already provide numerical potency predictions. However, the Bayesian approach may have potential for those chemicals where a chemistry modeling approach cannot provide a complete answer (e.g. pro-electrophiles whose in cutaneo activation cannot currently be modeled confidently). Nonetheless, our main message is of the importance of leveraging chemistry insights and read-across approaches to the fullest extent possible.