Separation of isotopologues of amphetamine with various degree of deuteration on achiral and polysaccharide-based chiral columns in high-performance liquid chromatography

Hydrogen/deuterium (H/D) isotope effects are not unusual in chromatography and such phenomena have been observed in both gas- and liquid-phase separations. Despite the numerous reports on this topic, the understanding of mechanisms and the underlying noncovalent interactions at play remains rather challenging. In our recent study, we reported baseline separation of isotopologoues of some amphetamine (AMP) derivatives on achiral and polysaccharide-based chiral columns, as well as some correlations between the degree of separation of enantiomers and isotopologues on (the same) polysaccharide-based chiral column(s). Following our previous findings on isotope effects in high-performance liquid chromatography, we report herein a comparative study on the isotope effects observed with AMP and methamphetamine (MET). The impact of some pivotal factors such as the number of deuterium atoms part of AMP isotopologues, the structure of its isotopomers, the chemical structure of the achiral and chiral stationary phases used in this study, and the use of methanol- vs acetonitrile-containing mobile phases on the isotope effects was examined and discussed. Quantitative correlations between the observed isotope effects and the enantioselectivity of the chiral columns used are also shortly discussed. Furthermore, considering the chromatographic results as benchmark experimental data, we attempted to elucidate the molecular bases of the observed phenomena using quantum mechanics calculations.

Molecular Tailoring Approach for the Direct Estimation of Individual Noncovalent Interaction Energies in Molecular Systems

The noncovalent interactions (NCIs) are omnipresent in chemistry, physics, and biology. The study of such interactions offers insights into various physicochemical phenomena. Some indirect approaches proposed in the literature for exploring the NCIs are briefly reviewed in Section 1 of this Perspective. These include: (i) Shift in the stretching frequency of an X-Y bond involved in X-Y···Z interaction. (ii) Topological analysis of molecular electron density. (iii) Empirical equations derived employing experimental and theoretical quantities. However, a direct method for estimating individual intramolecular/intermolecular interaction energies has been conspicuous by its absence from the literature. We have developed a molecular tailoring approach (MTA)-based method enabling a direct and reliable estimation of the energy of intra- as well as intermolecular interactions. This method offers a direct and reliable estimation of these interactions, in particular of the hydrogen bonds (HB) in molecules/weakly bound clusters along with the respective cooperativity contribution. In Section 2, the basis of our method is discussed, along with some illustrative examples. The application of this method to a variety of molecules and clusters, with a special emphasis on estimating the HB energy along with the energy of other NCIs is presented in Section 3. Section 4 discusses some computational strategies for applying our method to large molecular clusters. The last Section provides a summary and a discussion on future developments.

Interaction between hydroxymethanesulfonic acid and several organic compounds and its atmospheric significance

The interactions of the micro-mechanism of hydroxymethanesulfonic acid (HMSA) with the typical small organic molecule in atmospheric (X = methanol, formaldehyde, formic acid, methyl formate, dimethyl ether, acetone) has been investigated by density functional theory (DFT), quantum theory of atoms in molecules (QTAIM), Generalized Kohn-Sham Enery Decomposition Analysis (GKS-EDA) and the atmospheric clusters dynamic code (ACDC). The results of DFT show that the stable six- to eight-membered ring structures are easily formed in HMSA-X clusters. According to the topological analysis results of the AIM theory and the IRI method, a strong hydrogen bonding interaction is present in the complex. GKS-EDA results show that electrostatic energy is the main contributor to the interaction energy as it accounts for 51 %-55 % of the total attraction energy. The evaporation rates of HMSA-HMSA and HMSA-HCOOH clusters were much lower than those of the other HMSA complexes. In addition, the Gibbs energy of formation (ΔG) of HMSA-X dimers is investigated under atmosphere temperature T = 217-298 K and p = 0.19-1.0 atm, the ΔG decreased with decreasing of the atmosphere temperature and increased with the decrease of atmospheric pressure, indicating that the low temperature and high pressure may significantly facilitate to the formation of dimers.

Hydrogen bond types which do not fit accepted definitions

There are various interactions that either partially fit or do not fit the currently accepted definitions of the hydrogen bond. However, they possess characteristics of this interaction. It seems that it is partly connected to the fact that these definitions are not precise. The typical 3c-4e (three centres - four electrons) A-H⋯B hydrogen bond is characterized by the single-atom A and B centres that are highly electronegative. On the other hand, non-typical interactions that do not fit the hydrogen bond definitions well are characterised by uncommon proton donors and/or proton acceptors. The cases of multi-centre proton acceptors, π-electron or σ-electron systems are well known - such interactions are designated as A-H⋯π and A-H⋯σ hydrogen bonds, respectively. However, the cases of interactions with the multi-centre proton donors and proton acceptors do not fit the majority of definitions of hydrogen bond. The π⋯H+⋯π system in the proton-bound homodimer of acetylene is an example. This system can be classified as a hydrogen bond according to the two-sites hydrogen bond, 2sHB, definition. There are various types of interactions discussed in this review; among them, those that are undoubtedly unclassified as hydrogen bonds, i.e., hydride bonds, and charge inverted hydrogen bonds, CIHBs. Special emphasis is also put here on the proton sponges and other systems such as the [FHF]- anion or [NgHNg]+ cation (Ng is the noble gas centre).

Modulating Hydrogen Shuttling in Ammonia by Neutral and Cationic Boron-Containing Frustrated Lewis Pairs (FLPs)

Xanthene-backbone FLPs featuring secondary borane functions -B(ArX)H (where ArX=C6F5 (ArF) or C6Cl5 (ArCl)) have been targeted through reactions of the dihydroboranes Me2S ⋅ BArXH2 with [4,5-xanth(PR2)Li]2 (R=Ph, iPr), and investigated in the synthesis of related cationic systems via hydride abstraction. The reactivity of these systems (both cationic and charge neutral) with ammonia have been probed, with a view to probing the potential for proton shuttling via N-H bond 'activation.' We find that in the case of four-coordinate boron systems (cationic or change neutral), the N-H linkage remains intact, supported by a NH⋅⋅⋅P hydrogen bond which is worth up to 17 kcal mol-1 thermodynamically, and enabled by planarization of the flexible xanthene scaffold. For cationic three coordinate systems, N-to-P proton transfer is viable, driven by the ability of the boron centre to stabilise the [NH2]- conjugate base through N-to-B π bonding. This proton transfer can be shown to be reversible in the presence of excess ammonia, depending on the nature of the B-bound ArX group. It is viable in the case of C6F5 substituents, but is prevented by the more sterically encumbering and secondary donor-stabilising capabilities of the C6Cl5 substituent.

Similarities and Differences of Hydridic and Protonic Hydrogen Bonding

Ab initio calculations were employed to investigate the interactions between selected electron-donating groups, characterized by M-H bonds (where M represents a transition metal and H denotes a hydridic hydrogen), and electron-accepting groups featuring both σ- and π-holes. The study utilized the ωB97X-D3BJ/def2-TZVPPD level of theory. Hydridic hydrogen complexes were found in all complexes with σ- and π-holes. A comparative analysis was conducted on the properties hydridic H-bond complexes, presented here and those studied previously, alongside an extended set of protonic H-bonds complexes. While the stabilization energies changes in M-H bond lengths, vibrational frequencies, intensities of the spectral bands, and charge transfer for these complexes are comparable, the nature of hydridic and protonic H-bonds fundamentally differ. In protonic H-bond complexes, the main stabilization forces arise from electrostatic contributions, while in hydridic H-bond complexes, dispersion energy, is the primary stabilization factor due to the excess of electrons and thus larger polarizability at hydridic H. The finding represents an important characteristic that distinguishes hydridic H-bonding from protonic H-bonds.

Systematic Study of Different Types of Interactions in α-, β- and γ-Cyclodextrin: Quantum Chemical Investigation

In this work, comprehensive ab initio quantum chemical calculations using the DFT level of theory were performed to characterize the stabilization interactions (H-bonding and hyperconjugation effects) of two stable symmetrical conformations of α-, β-, and γ-cyclodextrins (CDs). For this purpose, we analyzed the electron density using "Atom in molecules" (AIM), "Natural Bond Orbital" (NBO), and energy decomposition method (CECA) in 3D and in Hilbert space. We also calculated the H-bond lengths and OH vibrational frequencies. In every investigated CD, the quantum chemical descriptors characterizing the strength of the interactions between the H-bonds of the primary OH (or hydroxymethyl) and secondary OH groups are examined by comparing the same quantity calculated for ethylene glycol, α-d-glucose (α-d-Glcp) and a water cluster as reference systems. By using these external standards, we can characterize more quantitatively the properties of these bonds (e.g., strength). We have demonstrated that bond critical points (BCP) of intra-unit H-bonds are absent in cyclodextrins, similar to α-d-Glcp and ethylene glycol. In contrast, the CECA analysis showed the existence of an exchange (bond-like) interaction between the interacting O…H atoms. Consequently, the exchange interaction refers to a chemical bond, namely the H-bond between two atoms, unlike BCP, which is not suitable for its detection.

From Short- to Long-Range Chiral Recognition on Surfaces: Chiral Assembly and Synthesis

Research on chiral behaviors of small organic molecules at solid surfaces, including chiral assembly and synthesis, can not only help unravel the origin of the chiral phenomenon in biological/chemical systems but also provide promising strategies to build up unprecedented chiral surfaces or nanoarchitectures with advanced applications in novel nanomaterials/nanodevices. Understanding how molecular chirality is recognized is considered to be a mandatory basis for such studies. In this review, a series of recent studies in chiral assembly and synthesis at well-defined metal surfaces under ultra-high vacuum conditions are outlined. More importantly, the intrinsic mechanisms of chiral recognition are highlighted, including short/long-range chiral recognition in chiral assembly and two main strategies to steer the reaction pathways and modulate selective synthesis of specific chiral products on surfaces.

Recent Advances in the Field of Amino Acid-Conjugated Aminoferrocenes-A Personal Perspective

The development of turn-based inhibitors of protein-protein interactions has attracted considerable attention in medicinal chemistry. Our group has synthesized a series of peptides derived from an amino-functionalized ferrocene to investigate their potential to mimic protein turn structures. Detailed DFT and spectroscopic studies (IR, NMR, CD) have shown that, for peptides, the backbone chirality and bulkiness of the amino acid side chains determine the hydrogen-bond pattern, allowing tuning of the size of the preferred hydrogen-bonded ring in turn-folded structures. However, their biological potential is more dependent on their lipophilicity. In addition, our pioneering work on the chiroptical properties of aminoferrocene-containing peptides enables the correlation of their geometry with the sign of the CD signal in the absorption region of the ferrocene chromophore. These studies have opened up the possibility of using aminoferrocene and its derivatives as chirooptical probes for the determination of various chirality elements, such as the central chirality of amino acids and the helicity of peptide sequences.

Hydrogen Bonds Are Never of an "Anti-electrostatic" Nature: A Brief Tour of a Misleading Nomenclature

A large amount of scientific works have contributed through the years to rigorously reflect the different forces leading to the formation of hydrogen bonds, the electrostatic and polarization ones being the most important among them. However, we have witnessed lately with the emergence of a new terminology, anti-electrostatic hydrogen bonds (AEHBs), that seems to contradict this reality. This nomenclature is used in the literature to describe hydrogen bonds between equally charged systems to justify the existence of these species, despite numerous proofs showing that AEHBs are, as any other hydrogen bond between neutral species, mostly due to electrostatic forces. In this Viewpoint, we summarize the state of the art regarding this issue, try to explain why this terminology is very misleading, and strongly recommend avoiding its use based on the hydrogen bond physical grounds.

Multiple hydrogen-bonded dimers: are only the frontier atoms relevant?

Non-frontier atom exchanges in hydrogen-bonded aromatic dimers can induce significant interaction energy changes (up to 6.5 kcal mol-1). Our quantum-chemical analyses reveal that the relative hydrogen-bond strengths of N-edited guanine-cytosine base pair isosteres, which cannot be explained from the frontier atoms, follow from the charge accumulation in the monomers.

Highly-ordered assembled organic fluorescent materials for high-resolution bio-sensing: a review

Organic fluorescent materials (OFMs) play a crucial role in the development of biosensors, enabling the extraction of biochemical information within cells and organisms, extending to the human body. Concurrently, OFM biosensors contribute significantly to the progress of modern medical and biological research. However, the practical applications of OFM biosensors face challenges, including issues related to low resolution, dispersivity, and stability. To overcome these challenges, scientists have introduced interactive elements to enhance the order of OFMs. Highly-ordered assembled OFMs represent a novel material type applied to biosensors. In comparison to conventional fluorescent materials, highly-ordered assembled OFMs typically exhibit robust anti-diffusion properties, high imaging contrast, and excellent stability. This approach has emerged as a promising method for effectively tracking bio-signals, particularly in the non-invasive monitoring of chronic diseases. This review introduces several highly-ordered assembled OFMs used in biosensors and also discusses various interactions that are responsible for their assembly, such as hydrogen bonding, π-π interaction, dipole-dipole interaction, and ion electrostatic interaction. Furthermore, it delves into the various applications of these biosensors while addressing the drawbacks that currently limit their commercial application. This review aims to provide a theoretical foundation for designing high-performance, highly-ordered assembled OFM biosensors suitable for practical applications. Additionally, it sheds light on the evolving trends in OFM biosensors and their application fields, offering valuable insights into the future of this dynamic research area.

Spirobifluorene-Based Porous Organic Salts: Their Porous Network Diversification and Construction of Chiral Helical Luminescent Structures

Porous organic salts (POSs) are organic porous materials assembled via charge-assisted hydrogen bonds between strong acids and bases such as sulfonic acids and amines. To diversify the network topology of POSs and extend its functions, this study focused on using 4,4',4'',4'''-(9,9'-spirobi[fluorene]-2,2',7,7'-tetrayl)tetrabenzenesulfonic acid (spiroBPS), which is a tetrasulfonic acid comprising a square planar skeleton. The POS consisting of spiroBPS and triphenylmethylamine (TPMA) (spiroBPS/TPMA) was constructed from the two-fold interpenetration of an orthogonal network with pts topology, which has not been reported in conventional POSs, owing to the shape of the spirobifluorene backbone. Furthermore, combining tris(4-chlorophenyl)methylamine (TPMA-Cl) and tris(4-bromophenyl)methylamine (TPMA-Br), which are bulkier than TPMA owing to the introduction of halogens at the p-position of the phenyl groups with spiroBPS allows us to construct novel POSs (spiroBPS/TPMA-Cl and spiroBPS/TPMA-Br). These POSs were constructed from a chiral helical network with pth topology, which was induced by the steric hindrance between the halogens and the curved fluorene skeleton. Moreover, spiroBPS/TPMA-Cl with pth topology exhibited circularly polarized luminescence (CPL) in the solid state, which has not been reported in hydrogen-bonded organic frameworks (HOFs).

Dynamics of Water Clusters Confined in Ionic Liquid at an Elevated Pressure

Over the years, numerous experimental and theoretical efforts have been dedicated to investigating the mysteries of water and determining its new unexplored physical properties. Despite this, high-pressure studies of water and aqueous mixtures close to the glass transition still represent an unknown area of research. Herein, we address a fundamental issue: the validity of the density scaling concept for fast water dynamics. For this purpose, we performed ambient and high-pressure dielectric measurements of a supercooled equimolar aqueous mixture of an acidic ionic liquid. All isothermal and isobaric relaxation data describing the time scale of charge transport (τσ) and fast dynamics within the water clusters (τν) reveal visual evidence of a liquid-glass transition. Furthermore, both relaxation processes satisfy the ργ/T scaling concept with a single exponent γ = 0.58. Thus, the scaling exponent is a state-point-independent parameter for the dynamics of water clusters confined in ionic liquid investigated in the pressure range up to 300 MPa.

Molecular dynamics and NMR reveal the coexistence of H-bond-assisted and through-space JFH coupling in fluorinated amino alcohols

The JFH coupling constants in fluorinated amino alcohols were investigated through experimental and theoretical approaches. The experimental JFH couplings were only reproduced theoretically when explicit solvation through molecular dynamics (MD) simulations was conducted in DMSO as the solvent. The combination of MD conformation sampling and DFT NMR spin-spin coupling calculations for these compounds reveals the simultaneous presence of through-space (TS) and hydrogen bond (H-bond) assisted JFH coupling between fluorine and hydrogen of the NH group. Furthermore, MD simulations indicate that the hydrogen in the amino group participates in both an intermolecular bifurcated H-bond with DMSO and in transmitting the observed JFH coupling. The contribution of TS to the JFH coupling is due to the spatial proximity of the fluorine and the NH group, aided by a combination of the non-bonding transmission pathway and the hydrogen bonding pathway. The experimental JFH coupling observed for the molecules studied should be represented as 4TS/1hJFH coupling.

Probing intramolecular interactions using molecular electrostatic potentials: changing electron density contours to unveil both attractive and repulsive interactions

We focus on intramolecular interactions, using the electrostatic potential plotted on iso-density surfaces to lead the way. We show that plotting the electrostatic potential on varying iso-density envelopes much closer to the nuclei than the commonly used 0.001 a.u. contour can reveal the driving forces for such interactions, whether they be stabilizing or destabilizing. Our approach involves optimizing the structures of molecules exhibiting intramolecular interactions and then finding the contour of the electronic density which allows the interacting atoms to be separated; we call this the nearly-touching contour. The electrostatic potential allows then to identify the intramolecular interactions as either attractive or repulsive. The discussed 1,5- and 1,6-intramolecular interactions in o-bromophenol and o-nitrophenol are attractive, while the interactions between terminal methyl hydrogens in diethyl disulfides (as shown recently) and those between the closest hydrogens in planar biphenyl and phenanthrene are clearly repulsive in nature. For the attractive 1,4-interactions in trinitromethane and chlorotrinitromethane, and the 1,3-S⋯N and the 1,4-Si⋯N interactions in the ClH2Si(CH2)nNH2 series, the lack of (3,-1) bond critical points has often been cited as reason to not identify such interactions as attractive in nature. Here, by looking at the nearly-touching contours we see that bond critical points are neither necessary nor sufficient for attractive interactions, as others have pointed out, and in some instances also pointing to repulsive interactions, as the examples of planar biphenyl and phenanthrene discussed in this work show.

Trialkylphosphonium Oxoborate as C(sp3 )-H Oxyanion Hole Catalyst for Diels-Alder Reaction

We have developed a catalytic protocol for Diels-Alder reaction using trialkylphosphonium oxoborates as oxyanion hole catalysts. The reaction can be operated under ambient conditions. Dienes could easily polymerize under acidic condition. Nonetheless, these acid-sensitive substrates are compatible with the catalytic protocol and the reaction scope covers a wide range of substrates.

Formic acid stability in different solvents by DFT calculations

CONTEXT

New technologies have been developed toward the use of green energies. The production of formic acid (FA) from carbon dioxide (CO[Formula: see text]) hydrogenation with H[Formula: see text] is a sustainable process for H[Formula: see text] storage. However, the FA adduct stabilization is thermodynamically dependent on the type of solvent and thermodynamic conditions. The results suggest a wide range of dielectric permittivity values between the dimethyl sulfoxide (DMSO) and water solvents to stabilize the FA in the absence of base. The thermodynamics analysis and the infrared and charge density difference results show that the formation of the FA complex with H[Formula: see text]O is temperature dependent and has a major influence on aqueous solvents compared to the FA adduct with amine, in good agreement with the experiment. In these conditions, the stability thermodynamic of the FA molecule may be favorable at non-organic solvents and dielectric permittivity values closer to water. Therefore, a mixture of aqueous solvents with possible ionic composition could be used to increase the thermodynamic stability of H[Formula: see text] storage in CO[Formula: see text] conversion processes.

METHODS

Using the Quantum ESPRESSO package, density functional theory (DFT) calculations were performed with periodic boundary conditions, and the electronic wave functions were expanded in plane waves. For the exchange-correlation functional, we use the vdW-DF functional with the inclusion of van der Waals (vdW) forces. Electron-ion interactions are treated by the projector augmented wave (PAW) method with pseudopotentials available in the PSlibrary repository. The wave functions and the electronic densities were expanded employing accurate cut-off energies of 6.80[Formula: see text]10[Formula: see text] and 5.44[Formula: see text]10[Formula: see text] eV, respectively. The electronic density was computed from the wave functions calculated at the [Formula: see text]-point in the first Brillouin-zone. Each structural optimization was minimized according to the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm, with force and energy convergence criteria of 25 meV[Formula: see text]Å[Formula: see text] and 1.36 meV, respectively. The electrostatic solvation effects were performed by the [Formula: see text] package with the Self-Consistent Continuum Solvation (SCCS) approach.

Quantification of hydrogen bond energy based on equations using spectroscopic, structural, QTAIM-based, and NBO-based descriptors which calibrated by the molecular tailoring approach

CONTEXT

Hydrogen bonds critically influence the structure and properties of both organic molecules and biomolecules, as well as supramolecular assemblies. For this reason, the development and elaboration of methods for quantitative assessment of hydrogen bond energy is an urgent challenge. In this study, using a large series of hydroxycarbonyl aliphatic compounds with the O‒H···O = C intramolecular hydrogen bond, a bank of hydrogen bond descriptors was created, including spectroscopic, structural, QTAIM-based, and NBO-based parameters. It was shown that the O‒H vibration frequency, OH chemical shift as the spectroscopic descriptors, the O···H hydrogen bond length, O···O distance, and O‒H covalent bond length as the structural descriptors, the electron density and its Laplacian, electron potential energy density in the hydrogen bond critical point, the electron density at the ring critical point as the QTAIM-based descriptors change in a correlated manner. The same correlation is found in change of the charge transfer energy through a hydrogen bond, the occupancy of the O‒H bond antibonding orbital, the Wiberg indices of the O···H hydrogen bond, and the O‒H covalent bond, as well as the polarization of the O‒H bond, which are the NBO-based descriptors. It was also recognized that the specified descriptors from the spectroscopic, structural, QTAIM-based, and NBO-based categories are functionally related to the values of intramolecular hydrogen bond energy, quantified via the molecular tailoring approach. This allowed one to obtain a system of equations for quantitative estimation of intramolecular hydrogen bond energy based on the spectroscopic, structural, QTAIM, and NBO descriptors, which makes such quantification more dependable and reliable.

METHODS

To obtain the spectroscopic descriptors, the vibrational spectra and shielding constants were calculated using the GIAO method. Structural descriptors were obtained for the equilibrium geometry of molecules, calculated at the MP2(FC)/6-311 +  + (2d,2p) level using the Gaussian 09 program. The QTAIM-based descriptors were calculated using the AIMAll program within the framework of the quantum theory "Atoms in Molecules." The NBO-based descriptors were calculated using the NBO 3.1 program implemented into Gaussian 09. To quantify the energy of intramolecular hydrogen bonds, molecular fragmentation was used within the molecular tailoring approach.

Recent advances in the utilization of covalent organic frameworks (COFs) as electrode materials for supercapacitors

Due to their excellent stability, ease of modification, high specific surface area, and tunable redox potentials, covalent organic frameworks (COFs) as potential electrodes in supercapacitors (SCs) have raised much research interest because these materials can enable the achievement of high electric double-layer supercapacitance and high pseudocapacitance. Here, the design strategies and SC applications of COF-based electrode materials are summarized. The detailed principles are introduced first, followed by discussions on strategies with diverse examples. The updated advances in design and applications are also discussed. Finally, in the outlook section, we provide some guidelines on the rational design of COF-based electrode materials for high-performance SCs, which we hope will inspire novel concepts for COF-based supercapacitors.

Dielectric Spectroscopy Studies of Conformational Relaxation Dynamics in Molecular Glass-Forming Liquids

We review experimental results obtained with broadband dielectric spectroscopy concerning the relaxation times and activation energies of intramolecular conformational relaxation processes in small-molecule glass-formers. Such processes are due to the interconversion between different conformers of relatively flexible molecules, and generally involve conformational changes of flexible chain or ring moieties, or else the rigid rotation of planar groups, such as conjugated phenyl rings. Comparative analysis of molecules possessing the same (type of) functional group is carried out in order to test the possibility of assigning the dynamic conformational isomerism of given families of organic compounds to the motion of specific molecular subunits. These range from terminal halomethyl and acetyl/acetoxy groups to both rigid and flexible ring structures, such as the planar halobenzene cycles or the buckled saccharide and diazepine rings. A short section on polyesters provides a generalisation of these findings to synthetic macromolecules.

Imaging of Single Molecular Behaviors Under Bifurcated Three-Centered Hydrogen Bonding

The mechanism for interaction and bonding of single guest molecules with active sites fundamentally determines the sorption and subsequent catalytic processes occurring in host zeolitic frameworks. However, no real-space studies on these significant issues have been reported thus far, since atomically visualizing guest molecules and recognizing single Al T-sites in zeolites remain challenging. Here, we atomically resolved single thiophene probes interacting with acid T-sites in the ZSM-5 framework to study the bonding behaviors between them. The synergy of bifurcated three-centered hydrogen bonds and van der Waals interactions can "freeze" the near-horizontal thiophene and make it stable enough to be imaged. By combining the imaging results with simulations, direct atomic observations enabled us to precisely locate the single Al T-sites in individual straight channels. Then, we statistically found that the thiophene bonding probability of the T11 site is 15 times higher than that of the T6 site. For different acid T-sites, the variation in the interaction synergy changes the inner angle of the host-guest O-H⋅⋅⋅S hydrogen bond, thereby affecting the stability of the near-horizontal thiophene and leading to considerable bonding inhomogeneities.

Trialkylphosphonium oxoborates as C(sp3)-H oxyanion holes and their application in catalytic chemoselective acetalization

The use of trialkylphosphonium oxoborates (TOB) as catalysts is reported. The site-isolated borate counter anion in a TOB catalyst increases the availability of C(sp3)-H to interact with electron donor substrates. The catalytic protocol is applicable to a wide range of substrates in the acetalization reaction and provides excellent chemoselectivity in the acetalization over thioacetalization in the presence of alcohols and thiols, which is otherwise hard to achieve using typical acid catalysts. Experimental and computational studies revealed that the TOB catalysts have multiple preorganized C(sp3)-Hs that serve as a mimic of oxyanion holes, which can stabilize the oxyanion intermediates via multiple C(sp3)-H non-classical hydrogen bond interactions.

Intermolecular interactions in clusters of ethylammonium nitrate and 1-amino-1,2,3-triazole

The intermolecular interaction energies, including hydrogen bonds (H-bonds), of clusters of the ionic liquid ethylammonium nitrate (EAN) and 1-amino-1,2,3-triazole (1-AT) based deep eutectic propellants (DeEP) are examined. 1-AT is introduced as a neutral hydrogen bond donor (HBD) to EAN in order to form a eutectic mixture. The effective fragment potential (EFP) is used to examine the bonding interactions in the DeEP clusters. The resolution of the Identity (RI) approximated second order Møller-Plesset perturbation theory (RI-MP2) and coupled cluster theory (RI-CCSD(T)) are used to validate the EFP results. The EFP method predicts that there are significant polarization and charge transfer effects in the EAN:1-AT complexes, along with Coulombic, dispersion and exchange repulsion interactions. The EFP interaction energies are in good agreement with the RI-MP2 and RI-CCSD(T) results. The quasi-atomic orbital (QUAO) bonding and kinetic bond order (KBO) analyses are additionally used to develop a conceptual and semi-quantitative understanding of the H-bonding interactions as a function of the size of the system. The QUAO and KBO analyses suggest that the H-bonds in the examined clusters follow the characteristic hydrogen bonding three-center four electron interactions. The strongest H-bonding interactions between the (EAN)1:(1-AT)n and (EAN)2:(1-AT)n (n = 1-5) complexes are observed internally within EAN; that is, between the ethylammonium cation [EA]+ and the nitrate anion ([NO3]-). The weakest H-bonding interactions occur between [NO3]- and 1-AT. Consequently, the average strengths of the H-bonds within a given (EAN)x:(1-AT)n complex decrease as more 1-AT molecules are introduced into the EAN monomer and EAN dimer. The QUAO bonding analysis suggests that 1-AT in (EAN)x:(1-AT)n can act as both a HBD and a hydrogen bond acceptor simultaneously. It is observed that two 1-AT molecules can form H-bonds to each other. Although the KBOs that correspond to H-bonding interactions in [EA]+:1-AT, [NO3]-:1-AT and between two 1-AT molecules are weaker than the H-bonds in EAN, those weak H-bond networks with 1-AT could be important to form a stable DeEP.

Novel Quinoline-Based Thiosemicarbazide Derivatives: Synthesis, DFT Calculations, and Investigation of Antitubercular, Antibacterial, and Antifungal Activities

The discovery of new antimicrobial agents as a means of treating drug-resistant microbial pathogens is of utmost significance to overcome their immense risk to human well-being. The current investigation involves the development, synthesis, and assessment of the antimicrobial efficacy of novel quinoline derivatives incorporating a thiosemicarbazide functionality. To design the target compounds (QST1-QST14), we applied the molecular hybridization approach to link various thiosemicarbazides to the quinoline core with a sulfonyl group. Upon the synthesis and completion of structural characterization via spectroscopic techniques (1H NMR, 13C NMR, 15N NMR, IR, and HRMS), the title molecules were extensively evaluated for their potential antitubercular, antibacterial, and antifungal activities. N-(3-Chlorophenyl)-2-(quinolin-8-ylsulfonyl)hydrazine-1-carbothioamide (QST4), the most effective compound against Mycobacterium tuberculosis H37Rv, was also tested on isoniazid-resistant clinical isolates with katG and inhA promoter mutations. Based on molecular docking studies, QST4 was also likely to demonstrate its antimycobacterial activity through inhibition of the InhA enzyme. Furthermore, three derivatives (QST3, QST4, and QST10) with preferable antimicrobial and drug-like profiles were also shown to be nontoxic against human embryonic kidney (HEK) cells. All compounds were optimized by the density functional theory method using B3LYP with the 6-31+G(d,p) basis set. Structural analysis, natural bond orbital calculations of donor-acceptor interactions, molecular electrostatic potential analysis, and frontier molecular orbital analysis were carried out. Quantum chemical descriptors and charges on the atoms were determined to compare the strengths of the intramolecular hydrogen bonds formed and their stabilities. We determined that the sulfur atom forms a stronger intramolecular hydrogen bond than the nitrogen, oxygen, and fluorine atoms in these sulfonyl thiosemicarbazide derivatives.

Hydrogen atoms in supramolecular chemistry: a structural perspective. Where are they, and why does it matter?

Hydrogen bonding interactions are ubiquitous across the biochemical and chemical sciences, and are of particular interest to supramolecular chemists. They have been used to assemble hydrogen bonded polymers, cages and frameworks, and are the functional motif in many host-guest systems. Single crystal X-ray diffraction studies are often used as a key support for proposed structures, although this presents challenges as hydrogen atoms interact only weakly with X-rays. In this Tutorial Review, we discuss the information that can be gleaned about hydrogen bonding interactions through crystallographic experiments, key limitations of the data, and emerging techniques to overcome these limitations.

The hydration of an oxy-polycyclic aromatic compound: the case of naphthaldehyde

The study of the intermolecular interactions of polycyclic aromatic compounds, considered as important pollutants of the Earth's atmosphere since they are emitted by the partial combustion of fuels, is essential to understand the formation and aging of their aerosols. In this study, the hydration of α-naphthaldehyde and β-naphthaldehyde isomers was investigated through a combination of Fourier transform microwave spectroscopy and quantum chemical calculations. Monohydrate structures were observed experimentally for both isomers, with two hydrate structures observed for β-naphthaldehyde and only one for α-naphthaldehyde, consistent with computational predictions. Analysis of the monohydrate structures indicated that the β-isomer exhibits higher hydrophilicity compared to the α-isomer, supported by electronic densities, hydration energies, and structural considerations. Further computational calculations were conducted to explore the planarity of the naphthaldehyde hydrates. Different levels of theory were employed, some of these revealing slight deviations from planarity in the hydrate structures. Low-frequency out-of-plane vibrational modes were examined, and the inertial defect was used to assess the planarity of the hydrates. The results suggested that the hydrates possess a predominantly planar structure, in agreement with the highest level of computational calculations and the absence of c-type transitions in the experimental spectra. Additionally, calculations were extended to dihydrate structures by attaching two water molecules to the naphthaldehyde isomers. The most stable dihydrate structures were predicted to be combinations of the observed monohydrate positions. However, experimental observation of the most stable dihydrate structures was challenging due to their very low vapour pressure, calling for complementary experiments using laser ablation nozzles.

Unified classification of non-covalent bonds formed by main group elements: a bridge to chemical bonding

Using correlation plots of binding energy and electron density at the bond critical point, we investigated the nature of intermolecular non-covalent bonds (D-X⋯A, where D = O/S/F/Cl/Br/H, mostly, X = main group elements (except noble gases), A = H2O, NH3, H2S, PH3, HCHO, C2H4, HCN, CO, CH3OH, and CH3OCH3). The binding energies were calculated at the MP2 level of theory, followed by Atoms in Molecules (AIM) analysis of the ab initio wave functions to obtain the electron density at the bond critical point (BCP). For each non-covalent bond, the slopes of the binding energy versus electron density plot have been determined. Based on their slopes, non-covalent bonds are classified as non-covalent bond closed-shell (NCB-C) or non-covalent bond shared-shell (NCB-S). Intriguingly, extrapolating the slopes of the NCB-C and NCB-S cases leads to intramolecular "ionic" and "covalent" bonding regimes, establishing a link between such intermolecular non-covalent and intramolecular chemical bonds. With this new classification, hydrogen bonds and other non-covalent bonds formed by a main-group atom in a covalent molecule are classified as NCB-S. Atoms found in ionic molecules generally form NCB-C type bonds, with the exception of carbon which also forms NCB-C type bonds. Molecules with a tetravalent carbon do behave like ions in ionic molecules such as NaCl and interact with other molecules through NCB-C type bonds. As with the chemical bonds, there are some non-covalent bonds that are intermediate cases.

Hydrogen Bonds in Lead Halide Perovskites: Insights from Ab Initio Molecular Dynamics

Hydrogen bonds (HBs) play an important role in the rotational dynamics of organic cations in hybrid organic/inorganic halide perovskites, thus affecting the structural and electronic properties of the perovskites. However, the properties and even the existence of HBs in these perovskites are not well established. In this study, we investigate HBs in perovskites MAPbBr3 (MA+ = CH3NH3+), FAPbI3 (FA+ = CH(NH2)2+), and their solid solution with composition (FAPbI3)7/8(MAPbBr3)1/8, using ab initio molecular dynamics and electronic structure calculations. We consider HBs donated by X-H fragments (X = N and C) of the organic cations and accepted by the halides (Y = Br and I) and characterize their properties based on pair distribution functions and on a combined distribution function of the hydrogen-acceptor distance with the donor-hydrogen-acceptor angle. By analyzing these functions, we establish geometrical criteria for HB existence based on the hydrogen-acceptor (H-Y) distance and donor-hydrogen-acceptor angle (X-H-Y). The distance condition is defined as d(H - Y) < 3 Å for N-H-donated HBs and d(H - Y) < 4 Å for C-H-donated HBs. The angular condition is 135° < (X - H - Y) < 180° for both types of HBs. A HB is considered to be formed when both angular and distance conditions are simultaneously satisfied. At the simulated temperature (350 K), the HBs dynamically break and form. We compute the time correlation functions of HB existence and HB lifetimes, which range between 0.1 and 0.3 ps at that temperature. The analysis of HB lifetimes indicates that N-H-Br bonds are relatively stronger than N-H-I bonds, while C-H-Y bonds are weaker, with a minimal influence from the halide and cation. To evaluate the impact of HBs on the vibrational spectra, we present the power spectrum in the region of N-H and C-H stretching modes, comparing them with the normal mode frequencies of isolated cations. We show that the peaks associated with N-H stretching modes in perovskites are redshifted and asymmetrically deformed, while the C-H peaks do not exhibit these effects.

Gas-Phase Room-Temperature Detection of the tert-Butyl Hydroperoxide Dimer

We have detected the tert-butyl hydroperoxide dimer, (t-BuOOH)2, in the gas phase at room temperature using conventional FTIR techniques. The dimer is identified by an asymmetric absorbance band assigned to the fundamental hydrogen-bound OHb-stretch. The weighted band maximum of the dimer OHb-stretch is located at ∼3452 cm-1, red-shifted by ∼145 cm-1 from the monomer OH-stretching band. The gas-phase dimer assignment is supported by Ar matrix isolation FTIR experiments at 12 K and experiments with a partially deuterated sample. Computationally, we find the lowest energy structure of (t-BuOOH)2 to be a doubly hydrogen bound six-membered ring with non-optimal hydrogen bond angles. We estimate the gas-phase constant of dimer formation, K, to be 0.4 (standard pressure of 1 bar) using the experimental integrated absorbance and a theoretically determined oscillator strength of the OHb-stretching band.

Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods

Hydrogen bonds play a critical role in the folding and stability of proteins, such as proteins and nucleic acids, by providing strong and directional interactions. They help to maintain the secondary and 3D structure of proteins, and structural changes in these molecules often result from the formation or breaking of hydrogen bonds. To gain insights into these hydrogen bonding networks, we applied two machine learning models - a logistic regression model and a decision tree model - to study four variants of thrombin: wild-type, ΔK9, E8K, and R4A. Our results showed that both models have their unique advantages. The logistic regression model highlighted potential key residues (GLU295) in thrombin's allosteric pathways, while the decision tree model identified important hydrogen bonding motifs. This information can aid in understanding the mechanisms of folding in proteins and has potential applications in drug design and other therapies. The use of these two models highlights their usefulness in studying hydrogen bonding networks in proteins.

Gauging the Strength of the Molecular Halogen Bond via Experimental Electron Density and Spectroscopy

Strong and weak halogen bonds (XBs) in discrete aggregates involving the same acceptor are addressed by experiments in solution and in the solid state. Unsubstituted and perfluorinated iodobenzenes act as halogen donors of tunable strength; in all cases, quinuclidine represents the acceptor. NMR titrations reliably identify the strong intermolecular interactions in solution, with experimental binding energies of approx. 7 kJ/mol. Interaction of the σ hole at the halogen donor iodine leads to a redshift in the symmetric C-I stretching vibration; this shift reflects the interaction energy in the halogen-bonded adducts and may be assessed by Raman spectroscopy in condensed phase even for weak XBs. An experimental picture of the electronic density for the XBs is achieved by high-resolution X-ray diffraction on suitable crystals. Quantum theory of atoms in molecules (QTAIM) analysis affords the electron densities and energy densities in the bond critical points of the halogen bonds and confirms stronger interaction for the shorter contacts. For the first time, the experimental electron density shows a significant effect on the atomic volumes and Bader charges of the quinuclidine N atoms, the halogen-bond acceptor: strong and weak XBs are reflected in the nature of their acceptor atom. Our experimental findings at the acceptor atom match the discussed effects of halogen bonding and thus the proposed concepts in XB activated organocatalysis.

Enhanced extraction of phenolic compounds from mango by-products using deep eutectic solvents

Deep eutectic solvents (DESs) potential for the extraction of polyphenolic compounds (PC) from mango by-products (peel and seed) was evaluated. Ultrasound (US) and agitation were applied to evaluate the effects of solvent and extraction methodology. The extracts were characterized with antioxidant capacity and HPLC-DAD profile. A theoretical study was performed using density functional theory and the QTAIM approach. β-alanine and choline chloride based DESs were effective to extract PC from peel and seed. Some DES increased PC extraction up to three times for peel (23.05 ± 1.22 mg/g DW) and up to five time for seeds (60.01 ± 1.40 mg/g DW). The PC profile varied with the solvent (DES vs EtOH/MeOH), procedure (US vs agitation) and material (peel or seed). Mangiferin extraction from peels was significantly increased with β-alanine based DES (676.08 ± 20.34 μg/gDW). The strength of H-bonds had a determining effect on the viscosity of DESs. The solute-solvent solvation energy was suitable to estimate the strength of H-bond interactions between DES and target compounds. This study demonstrates the remarkable capacity of DESs to extract PC from mango by-products and provides insights into the factors controlling extraction properties.

Radial distribution and hydrogen bonded network graphs of alcohol-aniline binary mixture

CONTEXT

Hydrogen bonds play a vital role in the stability and functioning of biomolecules. Suitable binary liquids are often used as prototypes for the study of biologically significant hydrogen bond studies and their intricate networks. Often, such systems show deviations in their physico-chemical properties from ideal conditions. As a continuation of our research interest in biologically important hydrogen-bonded systems, this paper reports the classical molecular dynamic studies on mixtures of aniline with 8 primary alcohols (C_RH_2R+1-OH, R = 1 to 8) for the complete concentration range. The energetics results indicate the predominance of OH--O interactions over other hydrogen bonds. Structures in the network are analyzed using radial distribution function (RDF), hydrogen bond statistics, and graph theoretical analysis (GTA). Coordination numbers, hydrogen bond statistics, and GTA show a bunching of alcohol-alcohol hydrogen bonds for lower aniline concentrations, while the aniline-aniline interactions are not affected by changes in the concentration.

METHODS

Interaction energies are calculated using B3LYP/6-311G++(d, p) density functional theory using Gaussian-09. The molecular dynamics simulations are carried out using GROMACS (V 2020.6) with the OPLS/AA force field and the simulation box is visualized using VMD. The NetworkX Python package is used for GTA calculation.

Understanding Nanocellulose-Water Interactions: Turning a Detriment into an Asset

Modern technology has enabled the isolation of nanocellulose from plant-based fibers, and the current trend focuses on utilizing nanocellulose in a broad range of sustainable materials applications. Water is generally seen as a detrimental component when in contact with nanocellulose-based materials, just like it is harmful for traditional cellulosic materials such as paper or cardboard. However, water is an integral component in plants, and many applications of nanocellulose already accept the presence of water or make use of it. This review gives a comprehensive account of nanocellulose-water interactions and their repercussions in all key areas of contemporary research: fundamental physical chemistry, chemical modification of nanocellulose, materials applications, and analytical methods to map the water interactions and the effect of water on a nanocellulose matrix.

Cyclodextrin regulated natural polysaccharide hydrogels for biomedical applications-a review

Cyclodextrin and its derivative (CDs) are natural building blocks for linking with other components to afford functional biomaterials. Hydrogels are polymer network systems that can form hydrophilic three-dimensional network structures through different cross-linking methods and are developing as potential materials in biomedical applications. Natural polysaccharide hydrogels (NPHs) are widely adopted in biomedical field with good biocompatibility, biodegradability, low cytotoxicity, and versatility in emulating natural tissue properties. Compared with conventional NPHs, CD regulated natural polysaccharide hydrogels (CD-NPHs) maintain good biocompatibility, while improving poor mechanical qualities and unpredictable gelation times. Recently, there has been increasing and considerable usage of CD-NPHs while there is still no review comprehensively introducing their construction, classification, and application of these hydrogels from the material point of view regarding biomedical fields. To draw a complete picture of the current and future development of CD-NPHs, we systematically overview the classification of CD-NPHs, and provide a holistic view on the role of CD-NPHs in different biomedical fields, especially in drug delivery, wound dressing, cell encapsulation, and tissue engineering. Moreover, the current challenges and prospects of CD-NPHs are discussed rationally, providing an insight into developing vibrant fields of CD-NPHs-based biomedicine, and facilitating their translation from bench to clinical medicine.

Cocrystals; basic concepts, properties and formation strategies

Cocrystallization is an old technique and remains the focus of several research groups working in the field of Chemistry and Pharmacy. This technique is basically in field for improving physicochemical properties of material which can be active pharmaceutical ingredients (APIs) or other chemicals with poor profile. So this review article has been presented in order to combine various concepts for scientists working in the field of chemistry, pharmacy or crystal engineering, also it was attempt to elaborate concepts belonging to crystal designing, their structures and applications. A handsome efforts have been made to bring scientists together working in different fields and to make chemistry easier for a pharmacist and pharmacy for chemists pertaining to cocrystals. Various aspects of chemicals being used as co-formers have been explored which predict the formation of co-crystals or molecular salts and even inorganic cocrystals.

Revealing the Reasons for Degeneration of Resonance-Assisted Hydrogen Bond on the Aromatic Platform: Calculations of Ortho-, Meta-, Para-Disubstituted Benzenes, and (Z)-(E)-Olefins

The energies of the O-H∙∙∙O=C intramolecular hydrogen bonds were compared quantitatively for the series of ortho-disubstituted benzenes and Z-isomers of olefins via a molecular tailoring approach. It was established that the hydrogen bond energy in the former series is significantly less than that in the latter one. The reason for lowering the hydrogen bond energy in the ortho-disubstituted benzenes compared to the Z-isomers of olefins is the decrease in the π-contribution to the total energy of the complex interaction, in which the hydrogen bond per se is enhanced by the resonance effect. By the example of the para- and meta-disubstituted benzenes, as well as E-isomers of olefins, it was explicitly shown that the aromatic ring is a much poorer conductor of the resonance effect compared to the double bond. The hydrogen bond in the ortho-disubstituted benzenes has a lower energy than a typical resonance-assisted hydrogen bond because the aromatic moiety cannot properly assist the hydrogen bond with a resonance effect. Thus, a hydrogen bond on an aromatic platform should fall into a special category, namely an aromaticity-assisted hydrogen bond, which is closer by nature to a simple hydrogen bond rather than to a resonance-assisted one.

Hydrogen bonding-induced high-performance stretchable organic semiconductors: a Review

Semiconductors are widely used in electron devices. With the development of wearable soft-electron devices, conventional inorganic semiconductors are unable to meet the demand because of their high rigidity and high cost. Thus, scientists construct organic semiconductors with high charge mobility, low cost, eco-friendly, stretchable, etc. Due to the excellent performance of stretchable organic semiconductors, they can be widely used as wearable soft-electron devices, such as stretchable organic field-effect transistors (OFETs), organic solar cells (OSCs), etc. Contains flexible display devices and flexible power sources, which are of great interest for applications of future electron devices. However, there are still some challenges that need to be solved. Commonly, enhancing the stretchability may cause the degradation of charge mobility, because of the destruction of the conjugated system. Currently, scientists find that hydrogen bonding can enhance the stretchability of organic semiconductors with high charge mobility. Thus in this review, based on the structure and design strategies of hydrogen bonding, various hydrogen bonding induced stretchable organic semiconductors are introduced. In addition, the applications of the hydrogen bonding induced stretchable organic semiconductors are reviewed. Finally, the stretchable organic semiconductors design concept and potential evolution trends are discussed. The final goal is to outline a theoretical scaffold for the design of high-performance wearable soft-electron devices, which can also further advance the development of stretchable organic semiconductors for applications.

Nature and Strength of Weak O⋅⋅⋅O Interactions in Nitryl Halide Dimers

The use of real space functions and molecular graphs has pushed some chemists to wonder: Are interactions between negatively charged oxygen atoms possible? In this contribution we analyze whether there is a real interaction between oxygen atoms in nitryl halide dimers (XNO₂ )₂ (X=F, Cl, Br and I) and in tetranitromethane and derivatives. Based on ab-initio and density functional theories (DFT) methods, we show these complexes are weakly stabilized. Energy decomposition analyses based on local molecular orbitals (LMOEDA) and interacting quantum atoms (IQA) reveal both dispersion and exchange play a crucial role in the stabilization of these complexes. Electron charge density and IQA analyses indicate that the oxygen atoms are connected by privileged exchange channels. In addition, electrostatic interactions between O and N atoms are also vital for the stabilization of the complexes. Finally, a reasonable explanation is given for the dynamic behavior of nitryl groups in tetranitromethane and derivatives.

Intrinsically Stretchable, Highly Efficient Organic Solar Cells Enabled by Polymer Donors Featuring Hydrogen-Bonding Spacers

Intrinsically stretchable organic solar cells (IS-OSCs), consisting of all stretchable layers, are attracting significant attention as a future power source for wearable electronics. However, most of the efficient active layers for OSCs are mechanically brittle due to their rigid molecular structures designed for high electrical and optical properties. Here, a series of new polymer donors (P_D s, PhAmX) featuring phenyl amide (N¹ ,N³ -bis((5-bromothiophen-2-yl)methyl)isophthalamide, PhAm)-based flexible spacer (FS) inducing hydrogen-bonding (H-bonding) interactions is developed. These P_D s enable IS-OSCs with a high power conversion efficiency (PCE) of 12.73% and excellent stretchability (PCE retention of >80% of the initial value at 32% strain), representing the best performances among the reported IS-OSCs to date. The incorporation of PhAm-based FS enhances the molecular ordering of P_D s as well as their interactions with a Y7 acceptor, enhancing the mechanical stretchability and electrical properties simultaneously. It is also found that in rigid OSCs, the PhAm5:Y7 blend achieves a much higher PCE of 17.5% compared to that of the reference PM6:Y7 blend. The impact of the PhAm-FS linker on the mechanical and photovoltaic properties of OSCs is thoroughly investigated.

Association Complexes of Calix[6]arenes with Amino Acids Explained by Energy-Partitioning Methods

Intermolecular complexes with calixarenes are intriguing because of multiple possibilities of noncovalent binding for both polar and nonpolar molecules, including docking in the calixarene cavity. In this contribution calix[6]arenes interacting with amino acids are studied with an additional aim to show that tools such as symmetry-adapted perturbation theory (SAPT), functional-group SAPT (F-SAPT), and systematic molecular fragmentation (SMF) methods may provide explanations for different numbers of noncovalent bonds and of their varying strength for various calixarene conformers and guest molecules. The partitioning of the interaction energy provides an easy way to identify hydrogen bonds, including those with unconventional hydrogen acceptors, as well as other noncovalent bonds, and to find repulsive destabilizing interactions between functional groups. Various other features can be explained by energy partitioning, such as the red shift of an IR stretching frequency for some hydroxy groups, which arises from their attraction to the phenyl ring of calixarene. Pairs of hydrogen bonds and other noncovalent bonds of similar magnitude found by F-SAPT explain an increase in the stability of both inclusion and outer complexes.

The Influence of the Halide in the Crystal Structures of 1-(2,3,5,6-Tetrafluoro-4-pyridyl)-3-benzylimidazolium Halides

The crystal structures of 1-(2,3,5,6-tetrafluoro-4-pyridyl)-3-benzylimidazolium chloride (1) and iodide (3) have been determined by single crystal X-ray diffraction. The crystal structure of 1 is similar to that of the bromide salt (2), possessing anion···C5F5N···C6H5 motifs, whilst that of 3 contains columns of alternating iodide anions and parallel tetrafluoropyridyl rings. All three crystal structures possess C(1)−H∙∙∙X− and C(2)−H∙∙∙X− hydrogen bonding. DFT calculations reveal that the strengths of the hydrogen bonding interactions lie in the order C(1)−H···X− > C(3)−H···X− > C(2)−H···X− for the same halide (X−) and Cl− > Br− > I− for each position. It is suggested that salt 3 adopts a different structure to salts 1 and 2 because of the larger size of iodide.

Hydrogen Bond Thermodynamics in Aqueous Acid Solutions: A Combined DFT and Classical Force-Field Approach

The thermodynamics of hydrogen bonds in aqueous and acidic solutions significantly impacts the kinetics and thermodynamics of acid reaction chemistry. We utilize in this work a multiscale approach, combining density functional theory (DFT) with classical molecular dynamics (MD) to model hydrogen bond thermodynamics in an acidic solution. Using thermodynamic cycles, we split the solution phase free energy into its gas phase counterpart plus solvation free energies. We validate this DFT/MD approach by calculating the aqueous phase hydrogen bond free energy between two water molecules (H₂O-···-H₂O), the free energy to transform an H₃O⁺ cation into an H₅O₂⁺ cation, and the hydrogen bond free energy of protonated water clusters (H₃O⁺-···-H₂O and H₅O₂⁺-···-H₂O). The computed equilibrium hydrogen bond free energy of H₂O-···-H₂O is remarkably accurate, especially considering the large individual contributions to the thermodynamic cycle. Turning to cations, we find the ion to be more stable than H₃O⁺ by roughly 1-2 k_BT. This small free energy difference allows for thermal fluctuation between the two idealized motifs, consistent with spectroscopic and simulation studies. Lastly, hydrogen bonding free energies between either H⁺ cation and H₂O in solution were found to be stronger than between two H₂O, though much less so than in vacuum because of dielectric screening in solution. Altogether, our results suggest the DFT/MD approach is promising for application in modeling hydrogen bonding and proton transfer thermodynamics in condensed phases.