Properties of the C−H···H Dihydrogen Bond: An ab Initio and Topological Analysis

Theoretical Insights into Regulation of Red/Blue-Shifting Hydrogen Bonds Through Cooperativity with Regium Bonds

To deeply understand the characteristics and regulation of red/blue-shifting hydrogen bonds (HBs), a theoretical investigation was conducted to explore the cooperativity between regium bonds and HBs in the complexes of Y···MCN···HCX3 (M = Cu, Ag, Au; Y = H2O, HCN, NH3; X = F, Cl). When MCN formed a hydrogen bonding dimer with CHF3 or CHCl3, the blue shift of C-H vibration frequency v(C-H) decreases as the following sequence Au > Cu > Ag, and the red shift decreases following the order Ag > Cu > Au. Upon the formation of ternary complexes, the presence of regium bonding interactions exerts a positive synergistic effect, resulting in the strengthening of the HBs. This, in turn, leads to noticeable changes in the red and blue shifts of v(C-H). In CHF3 complexes, v(C-H) undergoes a decrease in the blue shift, whereas that in CHCl3 exhibits an increase in the red shift. Especially, a transition from blue to red shift is observed within the AuCN···HCCl3 complex. As the strength of the regium bond increases, the trend of shifting from blue to red becomes more pronounced. For a given MCN, the changes occur in the order of NH3 > HCN > H2O. The interplay between two interactions was revealed by the molecular electrostatic potentials (MEP), the atoms in the molecule (AIM), and natural bond orbitals (NBO) analysis. It is revealed that Δv(C-H) is linearly correlated with a series of configuration and energy parameters. We explain the red- and blue-shifting HBs and their changes from the perspective of hyperconjugation and rehybridization. The presence of the positive synergistic effect enhances the hyperconjugation effect, thereby leading to a reduction in the blue shift and an increase in the red shift of v(C-H) within the complexes. This study enriches previous mechanisms regarding red- and blue-shifting HBs and introduces a novel idea to manipulate the characteristics of HBs, with the potential to impact the functioning of intricate systems.

Response surface and DFT protocols for improvement of the adsorption process of lignocellulosic-based biomass for the removal of basic dyes

Jatobá-do-cerrado fruit shells, archetypical of lignocellulosic-based biomass, were used as an adsorbent to remove crystal violet (CV) and methylene blue (MB) from water. The adsorbent was characterized using various techniques, and kinetic studies showed dye adsorption followed second-order kinetics. An experimental design investigated the effects of pH and temperature on removal efficiency, with a quadratic model fitting the data best. The results suggest pH influences MB's adsorption capacity more than temperature and at 25 °C and pH 8, MB had a desirability value of 0.89, with 95 % removal efficiency. For CV, temperature had a greater influence, with a desirability value of 0.874 at 25 °C and pH 10, and 95 % removal efficiency. Adsorption isotherm studies revealed maximum adsorption capacities of 123.0 mg·g-1 and 113.0 mg·g-1 for CV and MB, respectively. Experimental thermodynamic parameters indicated an endothermic and spontaneous process which it was supported by quantum chemistry calculations. The protocols developed confirmed the potential for adsorbing CV and MB dyes in water, achieving over 73.1 and 74.4 mg g-1 dyes removal.

Structural and decomposition analysis of TKX-50 with vacancy defects: insights from DFT and AIMD simulations

Vacancy defects are commonly present in crystals of energetic materials, and significantly influence the structural stability and decomposition mechanisms. However, there is a lack of profound understanding regarding the introduction of vacancy defects in energetic ionic salt, dihydroxylammonium 5,5'-bitetrazole-1,1'-dioxide (TKX-50). Due to the 1 : 2 ratio of anions to cations, TKX-50 possesses a more complex distribution of vacancy defects compared to traditional energetic materials. Based on the density functional theory method, the relatively favorable thermodynamic formation of vacancy defect distributions was revealed. The noncovalent interactions within the system, as well as the planarity of the anions, were investigated to understand the structural stability of TKX-50. Through ab initio molecular dynamics simulations, we discovered that vacancy defects can expedite the proton transfer during the initial decomposition stage of TKX-50 and affect the pathways of proton transfer. In the subsequent decomposition process, introduction of vacancy defects in the TKX-50 crystal leads to an earlier onset of ring-opening reactions and accelerates the appearance of decomposition products. The findings have the potential to provide insights into modeling vacancy defects in energetic ionic salts and reveal the impact of such defects on the structural stability and decomposition mechanisms of these materials.

Investigations of the reaction mechanism of sodium with hydrogen fluoride to form sodium fluoride and the adsorption of hydrogen fluoride on sodium fluoride monomer and tetramer

CONTEXT

The reaction between Na and HF is a typical harpooning reaction which is of great interest due to its significance in understanding the elementary chemical reaction kinetics. This work aims to investigate the detailed reaction mechanisms of sodium with hydrogen fluoride and the adsorption of HF on the resultant NaF as well as the (NaF)4 tetramer. The results suggest that the reaction between Na and HF leads to the formation of sodium fluoride salt NaF and hydrogen gas. Na interacts with HF to form a complex HF···Na, and then the approaching of F atom of HF to Na results in a transition state H···F···Na. Accompanied by the broken of H-F bond, the bond forms between F and Na atoms as NaF, then the product NaF is yielded due to the removal of H atom. The resultant NaF can further form (NaF)4 tetramer. The interaction of NaF with HF leads to the complex NaF···HF; the form I as well as II of (NaF)4 can interact with HF to produce two complexes (i.e., (NaF)4(I-1)···HF, (NaF)4(I-2)···HF, (NaF)4(II-1)···HF and (NaF)4(II-2)···HF), but the form III of (NaF)4 can interact with HF to produce only one complex (NaF)4(III)···HF. These complexes were explored in terms of noncovalent interaction (NCI) and quantum theory of atoms in molecules (QTAIM) analyses. NCI analyses confirm the existences of attractive interactions in the complexes HF···Na, NaF···HF, (NaF)4(I-1)···HF, (NaF)4(I-2)···HF, (NaF)4(II-1)···HF and (NaF)4(II-2)···HF, and (NaF)4(III)···HF. QTAIM analyses suggest that the F···Na interaction forms in the HF···Na complex while the F···H hydrogen bonds form in NaF···HF, (NaF)4(I-1)···HF, (NaF)4(I-2)···HF, (NaF)4(II-1)···HF and (NaF)4(II-2)···HF, and (NaF)4(III)···HF complexes. Natural bond orbital (NBO) analyses were also applied to analyze the intermolecular donor-acceptor orbital interactions in these complexes. These results would provide valuable insight into the chemical reaction of Na and HF and the adsorption interaction between sodium fluoride salt and HF.

METHODS

The calculations were carried out at the M06-L/6-311++G(2d,2p) level of theory which were performed using the Gaussian16 program. Intrinsic reaction coordinate (IRC) calculations were carried out at the same level of theory to confirm that the obtained transition state was true. The molecular surface electrostatic potential (MSEP) was employed to understand how the complex forms. Quantum theory of atoms in molecules (QTAIM) and noncovalent interaction (NCI) analysis was used to know the topology parameters at bond critical points (BCPs) and intermolecular interactions in the complex and intermediate. The topology parameters and the BCP plots were obtained by the Multiwfn software.

Enhanced dissolution of galactomannan and highly efficient selenium functionalization using ionic liquids with dual roles as solvents and catalysts

Galactomannan stands as a promising heteropolysaccharide, yet its randomly distributed non-linear structures and high molecular mass remain a huge challenge in solubilization and wide range of chemical modifications. This work develops a task specific approach for efficient dissolve of galactomannan in ionic liquids (ILs) by destructing and reconstructing intermolecular/intramolecular hydrogen bonds of galactomannan. Combining density functional theory calculations and experimental results, a reasonable mechanism of polysaccharide dissolution is proposed that the hydrogen bond networks of polysaccharide are broken, thus the hydroxyl groups are fully exposed and activated to facilitate functionalization. In view of the enhanced solubilization, an excellent effect in selenylation of galactomannan is notably improved by employing ILs with dual roles as solvents and catalysts. Typically, the introduction of -SO3H in ILs (SFILs) effectively enhances the protonation ability of selenium donor and thus further improves the functionalization efficiency. Furthermore, a surprising finding is observed that selenium content and average molecular mass of functionalized polysaccharide can be manipulated by the anions-cations synergistic effect which is highly dependent on SFILs acidity strength. This work proposed an integrated and promising strategy for improving the solubilization and functionalization manipulating by ILs, showing a great referential value for the widespread application in polysaccharide-rich resources.

First-row transition metal carbide nanosheets as high-performance cathode materials for lithium-sulfur batteries

Despite the prodigious potential of lithium-sulfur (Li-S) batteries as future rechargeable electrochemical systems, their commercial implementation is hindered by several vital issues, including the shuttle effect and sluggish migration of lithium-polysulfides leading to rapid capacity fading. Here, we systematically investigate the potential of first-row two-dimensional transition metal carbides (TMCs) as sulfur cathodes for Li-S batteries. The adsorption strength of lithium-polysulfides on TMCs is induced by the amount of charge transfer from the former to the latter and the proposed periodic relationship between sulfur in Li2S and 3d-transition metals. Our findings show that the VC nanosheet possesses immense anchoring potential and exhibits a comparatively low migration energy barrier for lithium-ion and Li2S molecules. Additionally, we report ab initio molecular dynamics simulations for lithiated polysulfide species anchored on a TMC-based model with a liquid-electrolyte medium. The microscopic reaction mechanism, revealed by the evolution of the reaction voltage during lithiation, demonstrates that the dissolution of high-order lithium-polysulfides in the electrolytes can be prevented due to their robust interaction with TMC-based cathode materials. These appealing features suggest that TMCs present colossal performance improvements for anchoring lithium-polysulfides, stimulating the active design of sulfur cathodes for practical Li-S batteries.

Experimental and Theoretical Study of the New Leveler Basic Blue 1 during Copper Superconformal Growth

A novel chlorinated functional group-modified triphenylmethane derivative leveler BB1 is used to achieve superconformal electrodeposition in microvias. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) are performed to study the suppressing effect of BB1, while the convection-dependent adsorption of BB1 on the copper surface is analyzed by galvanostatic measurement, and a BB1 concentration window between 100 and 200 mg/L is beneficial for superfilling. The interactions among BB1, bis-(sodium sulfopropyl) disulfide (SPS), and poly(ethylene glycol) (PEG) are also investigated. Density functional theory (DFT) calculation and in situ Raman spectroscopy are coupled to study the suppression mechanism and synergistic suppression mechanism, namely, the adsorption effect between BB1 and copper substrate, as well as the coordination effect between the modified chlorinated functional group and Cu2+, is proposed. The copper layer becomes smoother and more compact with an increase in BB1 concentration, according to scanning electron microscopy (SEM) and atomic force microscopy (AFM), while X-ray diffraction (XRD) analysis shows that the introduction of BB1 is conducive to the formation of the copper (220) plane. Besides, the solution wettability is boosted by BB1. A copper interconnecting layer with high quality is achieved with 150 mg/L BB1, while the surface deposition thickness (SDT) is about 34 μm and filling percentages (FPs) for microvias with diameters of 100, 125, and 150 μm are 81.34, 82.72, and 81.39%, respectively.

Synergistic mechanism of formaldehyde adsorption by intrinsic defects and carboxyl groups on the surface of carbon materials

The adsorption of formaldehyde on the original carbon material is limited. Determining the synergistic adsorption of formaldehyde by different defects on the carbon material is necessary for comprehensively understanding the mechanism of formaldehyde adsorption on the surface of the carbon material. The synergistic effect of intrinsic defects and oxygen-containing functional groups on formaldehyde adsorption on the surface of carbon materials was simulated and verified by experiments. Based on the density functional theory, the adsorption of formaldehyde on different carbon materials was simulated by quantum chemistry. The synergistic adsorption mechanism was studied by energy decomposition analysis, IGMH, QTAIM, and charge transfer, and the binding energy of hydrogen bonds was estimated. The results showed that the energy for the adsorption of formaldehyde adsorbed by the carboxyl group on the vacancy defect was the highest, at -11.86 kcal/mol, the hydrogen bond binding energy was -9.05 kcal/mol, and a larger charge transfer was recorded. The mechanism of synergy was studied comprehensively, and the simulation results were verified at multiple scales. This study provides valuable insights into the effect of carboxyl groups on the adsorption of formaldehyde by activated carbon.

Triel Bonds with Au Atoms as Electron Donors

The novel triel bonds of BX₃ (X=H, F, Cl, Br, and I) and C₅ H₅ B as electron acceptors and AuR₂ (R=Cl and CH₃ ) as an electron donor were explored. The triel bond is a primary driving force for most complexes, while the contribution from a halogen-chlorine interaction in BX₃ -AuCl₂ (X=Cl, Br, and I) and an iodine-Au interaction in BI₃ -Au(CH₃ )₃ is also very important. Interestingly, the positively charged Au atom of AuCl₂ can attractively bind with the holes of BX₃ and C₅ H₅ B. The interaction energy lies in the range of 1 and 80 kcal/mol, in the order X=F<H<Cl<Br<I. In most cases, the triel bond of C₅ H₅ B is stronger than the triel bond of BX₃ . In the formation of B-Au triel bond, electrostatic energy is not dominant, while polarization energy including orbital interaction has the largest contribution for the strongly bonded complexes and dispersion energy for the weak triel bond.

Cellulose Regeneration in Imidazolium-Based Ionic Liquids and Antisolvent Mixtures: A Density Functional Theory Study

Cellulose can be dissolved in ionic liquids (ILs), and it can be recovered by adding antisolvent such as water or alcohol. In addition, the regenerated cellulose can be used for textiles, degradable membranes, hydrogels/aerogels, etc. However, the regenerated mechanism of cellulose remains ambiguous. In this work, density functional theory (DFT) calculation is reported for the cellulose regeneration from a cellulose/1-n-butyl-3-methylimidazolium acetate (BmimOAc)/water mixture. To investigate the microscopic effects of the antisolvents, we analyzed the structures and H-bonds of BmimOAc-nH₂O and cellobiose-ILs-nH₂O (n = 0-6) clusters. It can be found that when n ≥ 5 in the BmimOAc-nH₂O clusters, the solvent-separated ion pairs (SIPs) play a dominant position in the system. With the increasing numbers of water molecules, the cation-anion interaction can be separated by water to reduce the effects of ILs on cellulose dissolution. Furthermore, the BmimOAc-nH₂O and cellobiose-ILs (n = 0-6) clusters tend to be a more stable structure with high hydration in an aqueous solution. When the water molecules were added to the system, H-bonds can be formed among H₂O, the hydroxyl of cellulose, and the oxygen of OAc. Therefore, the interactions between cellulose and ILs will be decreased to promote cellulose regeneration. This work would provide some help to understand the mechanism of cellulose regeneration from the view of theoretical calculation.

Xanthine oxidase inhibitory study of eight structurally diverse phenolic compounds

This project was designed to explore the xanthine oxidase (XO) inhibitory mechanism of eight structurally diverse phenolic compounds [quercetin: C1, quercetin-3-rhamnoside: C2, 4, 5-O-dicaffeoylquinic acid: C3, 3, 5-O-dicaffeoylquinic acid: C4, 3, 4-O-di-caffeoylquinic acid: C5, 4-O-caffeoylquinic acid (C6), 3-O-caffeoylquinic acid: C7, and caffeic acid: C8]. For this purpose, in-vitro and different computational methods were applied to determine the xanthine oxidase (XO) inhibitory potential of eight structurally diverse phenolic compounds. The results revealed that phenolic compounds (C1–C8) possess strong to weak XO inhibitory activity. These results were further confirmed by atomic force microscopy (AFM) and ¹H NMR analysis. Furthermore, computational study results revealed that phenolic compounds (C1–C8) bind with the surrounding amino acids of XO at the molybdenum (MO) site. These in-vitro and in-silico results divulge that phenolic compounds have a strong potential to lower uric acid levels via interacting with the XO enzyme and can be used to combat hyperuricemia.

Triel Bond Formed by Malondialdehyde and Its Influence on the Intramolecular H-Bond and Proton Transfer

Malondialdehyde (MDA) engages in a triel bond (TrB) with TrX₃ (Tr = B and Al; X = H, F, Cl, and Br) in three modes, in which the hydroxyl O, carbonyl O, and central carbon atoms of MDA act as the electron donors, respectively. A H···X secondary interaction coexists with the TrB in the former two types of complexes. The carbonyl O forms a stronger TrB than the hydroxyl O, and both of them are better electron donors than the central carbon atom. The TrB formed by the hydroxyl O enhances the intramolecular H-bond in MDA and thus promotes proton transfer in MDA-BX₃ (X = Cl and Br) and MDA-AlX₃ (X = halogen), while a weakening H-bond and the inhibition of proton transfer are caused by the TrB formed by the carbonyl O. The TrB formed by the central carbon atom imposes little influence on the H-bond. The BH₂ substitution on the central C-H bond can also realise the proton transfer in the triel-bonded complexes between the hydroxyl O and TrH₃ (Tr = B and Al).

Harnessing Greenhouse Gases Absorption by Doped Fullerenes with Externally Oriented Electric Field

In this work, a theoretical investigation of the effects caused by the doping of C₂₀ with silicon (Si) atom as well as the adsorption of CO, CO₂ and N₂ gases to C₂₀ and C₁₉Si fullerenes was carried out. In concordance with previous studies, it was found that the choice of the doping site can control the structural, electronic, and energetic characteristics of the C₁₉Si system. The ability of C₂₀ and C₁₉Si to adsorb CO, CO₂ and N₂ gas molecules was evaluated. In order to modulate the process of adsorption of these chemical species to C₁₉Si, an externally oriented electric field was included in the theoretical calculations. It was observed that C₁₉Si is highly selective with respect to CO adsorption. Upon the increase of the electric field intensity the adsorption energy was magnified correspondingly and that the interaction between CO and C₁₉Si changes in nature from a physical adsorption to a partial covalent character interaction.

Influence of phenolic acids/aldehydes on color intensification of cyanidin-3-O-glucoside, the main anthocyanin in sugarcane (Saccharum officinarum L.)

Sugarcane contains various anthocyanins, which are responsible for the colors present in sugarcane. In this study, the color intensification of the major anthocyanin, cyanidin-3-O-glucoside, by phenolic acids/aldehydes (ferulic acid, vanillic acid, p-coumaric acid, syringic aldehyde and vanillic aldehyde) was investigated. The color enhancement of cyanidin-3-O-glucoside (hyperchromic effect and bathochromic shift) was affected by the temperature and concentration of phenolic acids/aldehydes present. Reactions were spontaneous and exothermic, as determined using different thermodynamic parameters (ΔG⁰, ΔH⁰, ΔS⁰). Quantum chemical calculations demonstrated their intermolecular interaction differences, and AIM analysis indicated that hydrogen bonds and van der Waals force interactions contributed to color. Pyranoanthocyanins derived from cyanidin-3-O-glucoside and ferulic/p-coumaric acids during storage were recognized as cyanidin-3-O-glucoside-vinylphenol and cyanidin-3-O-glucoside-vinylguaiacol, respectively, by UPLC-ESI-QTOF-MS/MS. The electron-donating substituents on the aromatic ring of ferulic/p-coumaric acids stabilized the intermediately formed carbenium ion. Decarboxylation and further oxidation of the pyran moieties to the aromatic heterocycles resulted in the final products.

A detailed kinetic study on the tautomerization reactions of barbituric acid: A combined DFT-QTAIM analysis

A detailed kinetic study on the tautomerization reactions of barbituric acid (BA) at elevated temperatures from 270 K up to 1000 K was performed in this work. The B3LYP/6-311 + G(3df,2p) density functional theory (DFT) calculations were performed to evaluate the rate constants of transition states (TS) conversions of the tautomerization reactions. The connections from a given TS to the corresponding local minima of the reactant and product sides were confirmed by means of employing the intrinsic reaction coordinate (IRC) method. Moreover, the quantum theory of atoms in molecules (QTAIM) approach was employed to analyze the molecular mechanisms of reactions. The effects of vibrational normal mode frequencies of the reactant and TS were investigated on the curvature of the corresponding Arrhenius plot in the presence and absence of the tunneling effect. For each tautomerization reaction, the investigated reaction was partitioned into three different stages and four zones. The obtained results were plotted along with the corresponding reaction coordinates for each reaction considering and comparing different factors in agreement with already affirmed concepts. As a consequence, details of performed kinetic study on the tautomerization reactions of BA were successfully provided in this work.

Computational Study of CO2 Reduction Catalyzed by Iron(I) Complex at Different Spin States: Cooperativity of Hydrogen Bonding and Auxiliary Group Effect

To explore alternative approaches to the CO₂ reduction to formate and provide an insight into the spin state effect on the CO₂ reduction, we theoretically designed a kind of low-valence iron(I) model complex, whose doublet, quartet, and sextet states are denoted as ² Fe(I), ⁴ Fe(I), and ⁶ Fe(I), respectively. This complex is featured with an iron(I) center, which bonds to a 1,2-ethanediamine (en) and a 2-hydroxy-biphenyl group. Reaction mechanisms for the CO₂ reduction to formate catalyzed by this iron(I) model complex were explored using density functional theory (DFT) computations. Studies showed that the univalent iron(I) compound can efficiently fix and activate a CO₂ molecule, whereas its oxidized forms with trivalent iron(III) or bivalent iron(II) cannot activate CO₂. For the iron(I) compound, it was found that the lowest spin state ² Fe(I) is the most favorable for the CO₂ reduction as the reactions barriers involving ² Fe(I), ⁴ Fe(I), and ⁶ Fe(I) are 25.6, 37.2, and 35.9 kcal/mol, respectively. Yet, a photosensitizer-free visible-light-mediated high-low spin shift from ⁴ Fe(I) and ⁶ Fe(I) to ² Fe(I) is likely through the reverse intersystem crossing (RIC) because the ⁴ Fe(I) and ⁶ Fe(I) compounds have strong absorption in the visible-light range. Notably, the synergistic interaction between the hydrogen bonding from the auxiliary hydroxyl group in the 2-hydroxy-biphenyl moiety to CO₂ and an intermediate five-membered ring promotes the proton transfer, leading to the formation of the -COOH moiety from CO₂ and the Fe-O bond. With the addition of H₂, one H₂ molecule is split by the Fe-O bond and thus serves as H atom sources for both the CO₂ reduction and the recovery of the auxiliary hydroxyl group. The present theoretical study provides a novel solution for the challenging CO₂ reduction, which calls for further experimental verifications.

Tetrel Bonds between Phenyltrifluorosilane and Dimethyl Sulfoxide: Influence of Basis Sets, Substitution and Competition

Ab initio calculations have been performed for the complexes of DMSO and phenyltrifluorosilane (PTS) and its derivatives with a substituent of NH₃, OCH₃, CH₃, OH, F, CHO, CN, NO₂, and SO₃H. It is necessary to use sufficiently flexible basis sets, such as aug’-cc-pVTZ, to get reliable results for the Si···O tetrel bonds. The tetrel bond in these complexes has been characterized in views of geometries, interaction energies, orbital interactions and topological parameters. The electron-donating group in PTS weakens this interaction and the electron-withdrawing group prominently strengthens it to the point where it exceeds that of the majority of hydrogen bonds. The largest interaction energy occurs in the p-HO₃S-PhSiF₃···DMSO complex, amounting to −122 kJ/mol. The strong Si···O tetrel bond depends to a large extent on the charge transfer from the O lone pair into the empty p orbital of Si, although it has a dominant electrostatic character. For the PTS derivatives of NH₂, OH, CHO and NO₂, the hydrogen bonded complex is favorable to the tetrel bonded complex for the NH₂ and OH derivatives, while the σ-hole interaction prefers the π-hole interaction for the CHO and NO₂ derivatives.

The physical nature of the interaction in DMSO extraction separation of C8H10 isomer/n-decane systems

In this study, the liquid-liquid equilibrium of DMSO-C₈H₁₀ aromatic isomer-n-decane systems was measured at 30 °C under atmospheric pressure at first, followed by Othmer-Tobias equation data reliability verification and NRTL/UNIQUAC activity coefficient model correlation. Moreover, intermolecular interaction energies and molecular polarity indexes (MPI) were calculated to interpret the extraction results. Finally, a set of wave function analyses was accomplished to elaborate the physical nature of the interaction in the DMSO extraction process. These investigations show that: (1) intermolecular interaction energy and the MPI results corroborate the aromatic and alkane extraction distribution coefficients well. (2) The interactions between aromatics and DMSO are weak hydrogen bonding and van der Waals (vdW) interactions. The attractive part mainly involves dispersion (49.57-53.30%) and electrostatic (35.49-37.83%) effects. (3) The interactions between aromatics and n-decane are vdW interactions, dominated by attractive dispersion (70.41-70.93%) and repulsive exchange effects.

Halogen Interactions in Halogenated Oxindoles: Crystallographic and Computational Investigations of Intermolecular Interactions

X-ray structural determinations and computational studies were used to investigate halogen interactions in two halogenated oxindoles. Comparative analyses of the interaction energy and the interaction properties were carried out for Br···Br, C-H···Br, C-H···O and N-H···O interactions. Employing Møller-Plesset second-order perturbation theory (MP2) and density functional theory (DFT), the basis set superposition error (BSSE) corrected interaction energy (E_int(BSSE)) was determined using a supramolecular approach. The E_int(BSSE) results were compared with interaction energies obtained by Quantum Theory of Atoms in Molecules (QTAIM)-based methods. Reduced Density Gradient (RDG), QTAIM and Natural bond orbital (NBO) calculations provided insight into possible pathways for the intermolecular interactions examined. Comparative analysis employing the electron density at the bond critical points (BCP) and molecular electrostatic potential (MEP) showed that the interaction energies and the relative orientations of the monomers in the dimers may in part be understood in light of charge redistribution in these two compounds.

Group 12 Carbonates and their Binary Complexes with Nitrogen Bases and FH2 Z Molecules (Z=P, As, Sb): Synergism in Forming Ternary Complexes

MCO₃ (M=Zn, Cd, Hg) forms a spodium bond with nitrogen-containing bases (HCN, NHCH₂ , NH₃ ) and a pnicogen bond with FH₂ Z (Z=P, As, Sb). The spodium bond is very strong with the interaction energy ranging from -31 kcal/mol to -56 kcal/mol. Both NHCH₂ and NH₃ have an equal electrostatic potential on the N atom, but the corresponding interaction energy is differentiated by 1.5-4 kcal/mol due to the existence of spodium and hydrogen bonds in the complex with NHCH₂ as the electron donor. The spodium bond is weakest in the HCN complex, which is not consistent with the change of the binding distance. The spodium bond becomes stronger in the CdCO₃ <ZnCO₃ <HgCO₃ sequence although the positive electrostatic potential on the Hg atom is smallest. This is because the electrostatic interaction is dominant in the spodium-bonded complexes of CdCO₃ and ZnCO₃ but the polarization interaction in that of HgCO₃ . The pnicogen bond is much weaker than the spodium bond and the former has a larger enhancement than the latter in the FH₂ Z⋅⋅⋅OCO₂ M⋅⋅⋅N-base ternary complexes.

Synthesis, characterization, and theoretical studies of the photovoltaic properties of novel reactive azonitrobenzaldehyde derivatives

All dyes conduct but at different degrees of absorption; it is interesting to study the degree of conductivity and absorptivity of novel reactive azo-dyes in respect to dye-sensitized solar cells (DSSCs) to ascertain their viability for such applications. In this study, four novel reactive azo-dyes were experimentally synthesized from p-aminobenzaldehyde, 4-amino-3-nitrobenzaldehyde, and aniline through series of condensation and coupling reactions. The various functional groups, molecular connectivities, and molecular weight of the various fragments of the synthesized dyes were elucidated using the GC-MS, FT-IR, UV-vis, and NMR respectively. The experimentally determined structures were modeled and investigated using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) approaches to computationally compute the electronic structure properties, reactivity, absorption and solvatochromism in four different phases: gas, ethanol, acetone, and water, and the photovoltaic properties for possible applications in dye-sensitized solar cells (DSSCs). By comparing the HOMO (E_H) and the LUMO (E_L) energies from the results obtained demonstrates that dye D has the highest E_L energy value of −2.48 eV with a relatively lowest E_H energy value of −5.63 eV such that it lies underneath the conduction band edge of TiO₂ which is necessary to enable charge regeneration. Pi-electron delocalization was observed from the natural bond orbital (NBO) calculations between the different aromatic rings with dye B and A having the relatively highest and least second-order stabilization energies between σ* → σ* and LP* → LP interacting orbitals respectively. It is also observed in all the solvents that the Gibbs free energy of injection (ΔG_inject) is greater than 0.2 eV and hence, all the studied azo structures in the four phases provided efficient electron injection and light harvesting efficiency (LHE), however, the value of ΔG_inject for dyes B and D is greatest in all the four phases and thus, provided the highest electron injection of all the dyes. From the fact-findings of quantum theory of atoms-in-molecules (QTAIM), dyes A and C have extra-stability due to their relatively high numbers of intramolecular H-bond interactions along with some additional intra-atomic bonding between atoms within the studied compounds. Hence, all the four dyes are good for DSSCs applications.

Four novel reactive azo-dyes were experimentally synthesized from p-aminobenzaldehyde, 4-amino-3-nitrobenzaldehyde, and aniline through series of condensation and coupling reactions, and their properties were assessed for possible application in dye-sensitized solar cells.

Diboron Bonds Between BX3 (X=H, F, CH3 ) and BYZ2 (Y=H, F; Z=CO, N2 , CNH)

The ability of B atoms on two different molecules to engage with one another in a noncovalent diboron bond is studied by ab initio calculations. Due to electron donation from its substituents, the trivalent B atom of BYZ₂ (Z=CO, N₂ , and CNH; Y=H and F) has the ability to in turn donate charge to the B of a BX₃ molecule (X=H, F, and CH₃ ), thus forming a B⋅⋅⋅B diboron bond. These bonds are of two different strengths and character. BH(CO)₂ and BH(CNH)₂ , and their fluorosubstituted analogues BF(CO)₂ and BF(CNH)₂ , engage in a typical noncovalent bond with B(CH₃ )₃ and BF₃ , with interaction energies in the 3-8 kcal/mol range. Certain other combinations result in a much stronger diboron bond, in the 26-44 kcal/mol range, and with a high degree of covalent character. Bonds of this type occur when BH₃ is added to BH(CO)₂ , BH(CNH)₂ , BH(N₂ )₂ , and BF(CO)₂ , or in the complexes of BH(N₂ )₂ with B(CH₃ )₃ and BF₃ . The weaker noncovalent bonds are held together by roughly equal electrostatic and dispersion components, complemented by smaller polarization energy, while polarization is primarily responsible for the stronger ones.

Rational Design and Experimental Research on the Self-Assembled System of Thermosensitive Molecularly Imprinted Polymers Formed by α-Lipoic Acid and N-Vinyl Caprolactam

In this paper, the main work was to study the theoretical self-assembly process of thermosensitive molecularly imprinted polymers (MIPs) for α-lipoic acid and to investigate thermosensitive functional monomers through density functional theory calculations (DFT) and intermolecular weak interaction analysis. The M06-2X/6-311+G (d, p) level was used to study the structural parameters, bonding sites, natural population analysis, binding energies ( $\Delta E$ ), atom in molecules (AIM), independent gradient model (IGM), and imprinted molar ratio. The results revealed that α-lipoic acid mainly interacted with N-vinyl caprolactam (NVCL) by weak hydrogen bonds, and the best conditions for MIP synthesis were an optimum molar ratio of 1 : 4 (α-lipoic acid/NVCL). The thermosensitive properties showed that the highest adsorption was at 40°C and the lowest adsorption was at 20°C; also, the MIPs released the intercepted α-lipoic acid inside polymers, and the lower critical solution temperatures (LCST) of MIPs and nonimprinted polymers (NIPs) are 25.7°C and 19.4°C, respectively. In this study, the thermosensitive MIPs displayed a different adsorption capacity towards NVCL, which could be applied for controlled separation and release of α-lipoic acid in different temperatures in a complex matrix.

Cooperation/Competition between Halogen Bonds and Hydrogen Bonds in Complexes of 2,6-Diaminopyridines and X-CY3 (X = Cl, Br; Y = H, F)

The DFT calculations have been performed on a series of two-element complexes formed by substituted 2,6-diaminopyridine (R−PDA) and pyridine (R−Pyr) with X−CY3 molecules (where X = Cl, Br and Y = H, F). The primary aim of this study was to examine the intermolecular hydrogen and halogen bonds in the condition of their mutual coexistence. Symmetry/antisymmetry of the interrelation between three individual interactions is addressed. It appears that halogen bonds play the main role in the stabilization of the structures of the selected systems. However, the occurrence of one or two hydrogen bonds was associated with the favourable geometry of the complexes. Moreover, the impact of different substituent groups attached in the para position to the aromatic ring of the 2,6-diaminopyridine and pyridine on the character of the intermolecular hydrogen and halogen bonds was examined. The results indicate that the presence of electron-donating substituents strengthens the bonds. In turn, the presence of electron-withdrawing substituents reduces the strength of halogen bonds. Additionally, when hydrogen and halogen bonds lose their leading role in the complex formation, the nonspecific electrostatic interactions between dipole moments take their place. Analysis was based on geometric, energetic, and topological parameters of the studied systems.

Revealing the Dynamic Process of Ion Pair Recognition by Calix[4]pyrrole: A Case Study of Cesium Chloride

Ion pair receptors based on meso-octamethylcalix[4]pyrrole (CP) have been extensively investigated over recent years. However, the nature of their ion pair recognition has barely been reported, even for CP itself. Herein, cesium chloride was used as a guest ion pair to investigate the dynamic process of ion pair recognition by CP, and the "capture-bind" mechanism for this process is proposed for the first time. The results reveal that Cs⁺ can be first captured by Cl^- at long distances, and then it is bound to the cavity through almost equal contributions of Cl^- and CP. Although the effective charge of Cl^- is obviously reduced by charge-transfer, the electrostatic interactions between Cl^- and Cs⁺ are still strong even at long distances in the presence of CP.

Strength of the [Z-I···Hal]- and [Z-Hal···I]- Halogen Bonds: Electron Density Properties and Halogen Bond Length as Estimators of Interaction Energy

Bond energy is the main characteristic of chemical bonds in general and of non-covalent interactions in particular. Simple methods of express estimates of the interaction energy, Eint, using relationships between Eint and a property which is easily accessible from experiment is of great importance for the characterization of non-covalent interactions. In this work, practically important relationships between Eint and electron density, its Laplacian, curvature, potential, kinetic, and total energy densities at the bond critical point as well as bond length were derived for the structures of the [Z-I···Hal]- and [Z-Hal···I]- types bearing halogen bonds and involving iodine as interacting atom(s) (totally 412 structures). The mean absolute deviations for the correlations found were 2.06-4.76 kcal/mol.

Graphical Transition Moment Decomposition and Conceptual Density Functional Theory Approaches to Study the Fundamental and Lower-Level Overtone Absorption Intensities of Some OH Stretching Vibrations

The investigation of electron density migrations caused by molecular structure changes is of central importance in various fields of chemistry. To address this topic in general and to study absorption intensities of vibrations, we analyze sensitive dipole moment functions (DMFs) of a molecule by combining the linear response function of conceptual DFT and bond dipoles separated by the quantum theory of atoms in molecules with a graphical transition moment decomposition scheme. The fundamental intensities of OH stretching vibrations depend strongly on the substituents but only weakly on the molecular conformations. Interestingly, in some alcohols, completely opposite trends have been observed for the lower-level overtone intensities: a weak substituent dependence but a stronger conformation dependence. It is well known that the formation of a hydrogen-bonded complex increases the OH stretching fundamental intensity, but less well known is the decrease in their overtone intensities. To investigate these characteristics comprehensively, we calculated their intensities (Δv = 1, 2, and 3) for conformers of ethanol and trifluoroethanol (TFE) and hydrogen-bonded phenol (PhOH) systems via the DFT method in the local mode model for the OH stretching coordinate ΔR. Their first and second derivatives of the electron density with respect to ΔR were calculated and interpreted using their bond moments. For ethanol and TFE, the OH, CC, and CH bond moments were found to make an important contribution to the molecular DMF derivatives parallel to the OH bond. The OH bond contributes only to the first derivative of DMF, and its conformational dependence is determined by the magnitude of the charge polarization of each structure. The electron density derivatives in the CC bond region were largely maintained during the internal rotation; thus, their conformation-dependent contributions were expressed by a geometrical factor of the CC bond direction. The CH bond at the antiperiplanar position of the OH bond was found to make a remarkably large contribution to the second derivative of DMF in the gauche conformer. The importance of electron density migration on substituents was also identified in the hydrogen-bonded phenol, in which the π-electron density change on the aromatic ring was clearly shown. This migration creates the DMF derivatives both perpendicular and parallel to the OH bond and strongly affects the absorption intensities. In all the cases, some bond moments on the substituents contribute to the first and second DMF derivatives in a structure-dependent manner, thus explaining their stereoelectronic effects.

Hydrogen bonding catalysis by water in epoxide ring opening reaction

Water can act as catalyst is perhaps the most intriguing property reported of this molecule in the last decade. However, despite being an integral part of many enzyme structures, the role of water in catalyzing enzymatic reactions remains sparsely studied. In a recent study, we have shown that the epoxide ring opening in aspartate proteases follows a two-step process involving water. In this work, we attempt to unravel the electronic basis of the co-catalytic role of water in the epoxide ring opening reaction by employing high-level quantum mechanical calculations at M06-2X/6-31+G(d,p) level of accuracy. Our computed electron density and its reduced gradient show that water anchor the reactant molecules through strong H-bond bridges. In addition, the strong ionizing power of water allows better charge delocalization to stabilize the transition states and oxyanion intermediate. Electrostatic analyses suggest greater charge transfer from the aspartates to the epoxide in the transition state, which is found to be exergonic in nature rendering a low-barrier reaction compared to a control system where water was omitted in the reaction field. This elucidated mechanism at electronic level could promote further research to search for the co-catalytic role of water in other enzymes.

High-energetic and low-sensitive 1,3,5-triamino 2,4,6-trinitrobenzene (TATB) crystal: first principles investigation and Hirshfeld surface analysis

The N–H⋯O hydrogen bonding between neighboring TATB molecules within a planar layer cooperates with π⋯π interaction between two adjacent molecules from two adjacent layers in the TATB crystal.

Halogen bonds on substituted dibromonitrobenzene derivatives

Halogen bonding is a noncovalent interaction that has attracted great attention because of its importance in several areas, such as photonics, nonlinear optics, pharmaceutical products, supramolecular engineering, biochemistry, protein-ligand complexes, and polymer interactions. In this context, we describe the synthesis, molecular structure, supramolecular arrangement, and theoretical calculations of five dibromonitrobenzene derivatives, which present different halogen atoms substituted. The solid-state characterization was carried out by X-ray diffraction with the contribution of Hirshfeld surfaces for analysis of molecular interactions. The frontier molecular orbital, molecular electrostatic potential, and quantum theory of atoms in molecules were carried out at the M06-2X/6-311+G(d,p) level of theory. Those observed halogen interactions indicate the crystalline solid-state stabilization for the dibromonitrobenzene derivatives.

Competition between the hydrogen bond and the halogen bond in a [CH3OH-CCl4] complex: a matrix isolation IR spectroscopy and computational study

Methanol (CH3OH) is the simplest alcohol and carbon tetrachloride (CCl4) is widely used as a solvent in the chemical industry. CH3OH and CCl4 are both important volatile substances in the atmosphere and CCl4 is an important precursor for atmospheric ozone depletion. Moreover, mixtures of CH3OH and CCl4 are an important class of non-aqueous mixtures as they exhibit a large deviation from Raoult's law. The specific interaction between CH3OH and CCl4 is not yet investigated experimentally. The interaction between CH3OH and CCl4 at the molecular level can be twofold: hydrogen bond (O-HCl) and halogen bond (C-ClO) interaction. One halogen bonded minimum and two hydrogen bonded minima are identified in the dimer potential energy surface. Herein, the 1 : 1 complex of [CH3OH-CCl4] has been characterised using matrix-isolation infrared spectroscopy and electronic structure calculations to investigate the competition between hydrogen bonded and halogen bonded complexes. Vibrational spectra have been monitored in the C-Cl, C-O, and O-H stretching regions. The exclusive formation of halogen bonded 1 : 1 complexes in argon and nitrogen matrices is confirmed by a combination of experimental and simulated vibrational frequency, stabilisation energy, energy decomposition analysis, and natural bond orbital and atoms-in-molecules analyses. This investigation helps to understand the specific interactions in the [CH3OH-CCl4] mixture and also the possibilities of formation of halogen bonded atmospheric complexes that may influence the atmospheric chemical activities, and enhance aerosol formation and deposition of CCl4.

Influence of N-Base and O-Base Hybridization on Triel Bonds

The complexes of TrR₃ (Tr = B and Al; R = H, F, Cl, and Br) with three N-bases (NH₃, CH₂NH, and HCN) and three O-bases (CH₃OH, H₂CO, and CO) are utilized to explore the hybridization effect of N and O atoms on the strength, properties, and nature of the triel bond. The sp-hybridized O and N atoms form the weakest triel bond, followed by the sp²-hybridized O atom or the sp³-hybridized N atom, and the sp³-hybridized O atom or the sp²-hybridized N atom engages in the strongest triel bond. The hybridization effect is also related to the substituent of TrR₃. Most complexes are dominated by electrostatic, with increasing polarization contribution from sp to sp² to sp³. Although the CO oxygen engages in a weaker triel bond, its carbon atom is a better electron donor and the interaction energy even amounts to -37 kcal/mol in the BH₃ complex.

Theoretical Insight into the Interaction between Chloramphenicol and Functional Monomer (Methacrylic Acid) in Molecularly Imprinted Polymers

Molecular imprinting technology is a promising method for detecting chloramphenicol (CAP), a broad-spectrum antibiotic with potential toxicity to humans, in animal-derived foods. This work aimed to investigate the interactions between the CAP as a template and functional monomers required for synthesizing efficient molecularly imprinted polymers for recognition and isolation of CAP based on density functional theory. The most suitable monomer, methacrylic acid (MAA), was determined based on interaction energies and Gibbs free energy changes. Further, the reaction sites of CAP and MAA was predicted through the frontier molecular orbitals and molecular electrostatic potentials. Atoms in molecules topology analysis and non-covalent interactions reduced density gradient were applied to investigate different types of non-covalent and inter-atomic interactions. The simulation results showed that CAP was the main electron donor, while MAA was the main electron acceptor. Moreover, the CAP–MAA complex simultaneously involved N-H···O and C=O···H double hydrogen bonds, where the strength of the latter was greater than that of the former. The existence of hydrogen bonds was also confirmed by theoretical and experimental hydrogen nuclear magnetic resonance and Fourier transform infrared spectroscopic analyses. This research can act as an important reference for intermolecular interactions and provide strong theoretical guidance regarding CAP in the synthesis of molecularly imprinted polymers.

Substituent effect on inter-ring interaction in paracyclophanes

The theoretical calculations, namely multipole-derived charge analysis, quantum theory of atom in molecules, and non-bonding interaction (NCI), were performed for [2.2]paracyclophanes, [2.2]paracyclophane-7,9-dienes, and [3.3]paracyclophanes optimized at B3LYP/6-311++G** level, including dispersion correction. The substituent effect of the electron donor N(Me)2 and electron acceptor NO2 group and the influence of the length of bridges joining the aromatic ring on aromatic ring interaction energy (AIE) and strain energy were discussed. The local and electrostatic character of the substituent effect in paracyclophanes was shown. The presence of the weak orbital through-space C···C interaction between the [3.3]paracyclophane ring and weak CH···O hydrogen bonds between the substituents in the different rings was shown.

Theoretical study on the microscopic mechanism of lignin solubilization in Keggin-type polyoxometalate ionic liquids

Keggin-type polyoxometalate derived ionic liquids (POM-ILs) have recently been presented as effective solvent systems for biomass delignification. To investigate the mechanism of lignin dissolution in POM-ILs, the system involving POM-IL ([C4C1Im]₃[PW₁₂O₄₀]) and guaiacyl glycerol-β-guaiacyl ether (GGE), which contains a β-O-4 bond (the most dominant bond moiety in lignin), was studied using quantum mechanical calculations and molecular dynamics simulations. These studies show that more stable POM-IL structures are formed when [C4C1Im]⁺ is anchored in the connecting four terminal oxygen region of the [PW₁₂O₄₀]^3- surface. The cations in POM-ILs appear to stabilize the geometry by offering strong and positively charged sites, and the POM anion is a good H-bond acceptor. Calculations of POM-IL interacting with GGE show the POM anion interacts strongly with GGE through many H-bonds and π-π interactions which are the main interactions between the POM-IL anion and GGE and are strong enough to force GGE into highly bent conformations. These simulations provide fundamental models of the dissolution mechanism of lignin by POM-IL, which is promoted by strong interactions of the POM-IL anion with lignin.