Kinetic study of the reaction of thiophene-tocopherols with peroxyl radicals enlightenings the role of O˙⋯S noncovalent interactions in H-atom transfer

Three new α-tocopherol thiophene derivatives were efficiently synthesized, characterized and used for the first time as chain-breaking antioxidants for the inhibition of the autoxidation of reference oxidizable substrates. The rate constant of the reaction with alkylperoxyl (ROO˙) radicals and the stoichiometry of radical trapping (n) for the thiophene-tocopherol compounds were determined by measuring the oxygen consumption during the autoxidation of styrene or isopropylbenzene, using a differential pressure transducer. The measurement of the reaction with ROO˙ radicals in an apolar solvent at 30 °C showed inhibition rate constants (kinh) in the order of 104 M-1 s-1. To rationalise the kinetic results, the effect of the thiophene ring on the H-atom donation by O-H groups of the functionalized tocopherols was investigated by theoretical calculations. The importance of noncovalent interactions (including an unusual O˙⋯S bond) for the stability of the conformers has been shown, and the O-H bond dissociation enthalpy (BDE(OH)) of these derivatives was determined. Finally, the photophysical properties of these new compounds were investigated to understand if the addition of thiophene groups changes the absorption or emission spectra of the tocopherol skeleton for their possible application as luminescent molecular probes.

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.

Structural Diversity of Protonated Citric Acid-Ammonia Clusters and Its Atmospheric Implication

Various acid-base molecular clusters involving organic species can serve as precursors that play important roles in the formation of an atmospheric aerosol. Due to its structural flexibility and its ability to form multiple hydrogen bonds, citric acid acts as a key species in forming clusters that are critical in the nucleation of related aerosol precursors. Thus, it is provoking to characterize the structures of these clusters at the molecular level. In this paper, protonated citric acid-ammonia clusters of various sizes were generated by electrospray ionization and studied by tandem mass spectrometry. The structures of [(CA)2+NH4]1+ and [(CA)4+NH4]1+ were further characterized by the method of infrared photodissociation (IRPD) spectroscopy. Combined with theoretical calculations, it is found that the most stable structures of the dimeric and tetrameric isomers show the shapes of an ingot and a lantern, respectively. It has been revealed that the temperature has a great effect on the contributions of different isomers for both dimers and tetramers. The dominat isomers are found to have more open structures at higher temperatures, facilitating the growth of clusters through new hydrogen bonds.

Methods to functionalize gold nanoparticles with tandem-phosphorothioate DNA: role of physicochemical properties of the phosphorothioate backbone in DNA adsorption to gold nanoparticles

Perception of the differences in the physicochemical properties of phosphorothioate DNA (PS-DNA) and phosphodiester DNA (PO-DNA) greatly aids in understanding the AuNP-DNA binding process. Replacing one non-bridging oxygen atom of the anionic phosphodiester backbone with a sulfur atom leads to a major change in the DNA adsorption mechanism of AuNPs. In this work, we investigated and compared salt-aging, low pH-assisted, and freeze-thaw methods for conjugating phosphorothioate-modified oligonucleotides to AuNPs. The results obtained clearly demonstrate that only the pH-assisted method can successfully bind tandem phosphorothioate DNA to gold nanoparticles and sufficiently maintain the colloidal stability of AuNPs. When a phosphate group is converted to a phosphorothioate group, the negative charge of the phosphate group is located on the sulfur atom. Due to the soft nature of sulfur (a very weak H-bond acceptor), the negative charge on the sulfur atom cannot be shielded even with the gradual addition of salt to increase the ionic strength, so, the pH-assisted based method is the best for the functionalization of AuNPs with tandem-PS DNA.

The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function

Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.

Sulfur atom modification on thymine improves the specificity and sensitivity of DNA polymerization and detection

The incorporation of STTP can significantly reduce the non-specific amplification products in DNA polymerase reaction.

Investigation of chalcogen bioisosteric replacement in a series of heterocyclic inhibitors of tryptophan 2,3-dioxygenase

Selenium is an underexplored element that can be used for bioisosteric replacement of lower molecular weight chalcogens such as oxygen and sulfur. More studies regarding the impact of selenium substitution in different chemical scaffolds are needed to fully grasp this element's potential. Herein, we decided to evaluate the impact of selenium incorporation in a series of tryptophan 2,3-dioxygenase (TDO2) inhibitors, a target of interest in cancer immunotherapy. First, we synthesized the different chalcogen isosteres through Suzuki-Miyaura type coupling. Next, we evaluated the isosteres' affinity and selectivity for TDO2, as well as their lipophilicity, microsomal stability and cellular toxicity on TDO2-expressing cell lines. Overall, chalcogen isosteric replacements did not disturb the on-target activity but allowed for a modulation of the compounds' lipophilicity, toxicity and stability profiles. The present work contributes to our understanding of oxygen/sulfur/selenium isostery towards increasing structural options in medicinal chemistry for the development of novel and distinctive drug candidates.

Supercritical fluid extraction-supercritical fluid chromatography of saliva: Single-quadrupole mass spectrometry monitoring of caffeine for gastric emptying studies†

Saliva is an attractive sampling matrix for measuring various endogenous and exogeneous substances but requires sample treatment prior to chromatographic analysis. Exploiting supercritical CO₂ for both extraction and chromatography simplifies sample preparation, reduces organic solvent consumption, and minimizes exposure to potentially infectious samples, but has not yet been applied to oral fluid. Here, we demonstrate the feasibility and benefits of online supercritical fluid extraction coupled to supercritical fluid chromatography and single-quadrupole mass spectrometry for monitoring the model salivary tracer caffeine. A comparison of ¹³ C- and ³² S-labeled internal standards with external standard calibration confirmed the superiority of stable isotope-labeled caffeine over nonanalogous internal standards. As proof of concept, the validated method was applied to saliva from a magnetic resonance imaging study of gastric emptying. After administration of 35 mg caffeine via ice capsule, salivary levels correlated with magnetic resonance imaging data, corroborating caffeine's usefulness as tracer of gastric emptying (R²  = 0.945). In contrast to off-line methods, online quantification required only minute amounts of organic solvents and a single manual operation prior to online bioanalysis of saliva, thus demonstrating the usefulness of CO₂ -based extraction and separation techniques for potentially infective biomatrices.

Synergistic effect of glutaric acid and ammonia/amine/amide on their hydrates in the clustering: A theoretical study

The formation of molecular clusters makes influence on the atmosphere. The clusters of glutaric acid (GA) and common ammonia (A), amine (methylamine MA, dimethylamine DMA) and representative amide (urea U) along with water molecule were systematically studied theoretically. GA-A-nW (n = 1, 2), GA-MA-nW (n = 1, 2), GA-DMA-1W and GA-U-nW (n = 1-6) are predicted to be feasible thermodynamically with the hydrogen bonds as interaction force. GA and urea promote the clustering synergistically, and ammonia, methylamine, dimethylamine promote the clustering of small GA hydrates (n = 1-2), while inhibit that of large GA hydrates (n = 3-6). The results of humidity show that un-hydrate or mono-hydrate is the main form of GA-mbase-nW (m = 0, 1; n = 1-6) under relative humidity of 20%, 50% and 80%. The global minima remain dominant over the temperature range of 220-320 K. GA contributes more to the Rayleigh scattering properties than sulfuric acid. More importantly, the local minima can undergo isomerization to form the global minima crossing a free energy barrier ranging from 6.66 to 11.78 kcal mol^-1. This study indicates that GA and base molecules play a synergistic role to promote the formation of clusters. We hope it can provide more insights on interesting clustering in theory.

O-H stretching frequency red shifts do not correlate with the dissociation energies in the dimethylether and dimethylsulfide complexes of phenol derivatives

In this perspective, we present a comprehensive report on the spectroscopic and computational investigations of the hydrogen bonded (H-bonded) complexes of Me2O and Me2S with seven para-substituted H-bond donor phenols. The salient finding was that although the dissociation energies, D0, of the Me2O complexes were consistently higher than those of the analogous Me2S complexes, the red-shifts in phenolic O-H frequencies, Δν(O-H), showed the exactly opposite trend. This is in contravention of the general perception that the red shift in the X-H stretching frequency in the X-HY hydrogen bonded complexes is a reliable indicator of H-bond strength (D0), a concept popularly known as the Badger-Bauer rule. This is also in contrast to the trend reported for the H-bonded complexes of H2S/H2O with several para substituted phenols of different pKa values wherein the oxygen centered hydrogen bonded (OCHB) complexes consistently showed higher Δν(O-H) and D0 compared to those of the analogous sulfur centered hydrogen bonded (SCHB) complexes. Our effort was to understand these intriguing observations based on the spectroscopic investigations of 1 : 1 complexes in combination with a variety of high level quantum chemical calculations. Ab initio calculations at the MP2 level and the DFT calculations using various dispersion corrected density functionals (including DFT-D3) were performed on counterpoise corrected surfaces to compute the dissociation energy, D0, of the H-bonded complexes. The importance of anharmonic frequency computations is underscored as they were able to correctly reproduce the observed trend in the relative OH frequency shifts unlike the harmonic frequency computations. We have attempted to find a unified correlation that would globally fit the observed red shifts in the O-H frequency with the H-bonding strength for the four bases, namely, H2S, H2O, Me2O, and Me2S, in this set of H-bond donors. It was found that the proton affinity normalized Δν(O-H) values scale very well with the H-bond strength.

The Characteristics of Disulfide-Centered Hydrogen Bonds

The disulfide-centered hydrogen bonds in the three different model systems of diethyl disulfide⋅⋅⋅H₂ O/H₂ CO/HCONH₂ clusters were characterized by high-resolution Fourier transform microwave spectroscopy and quantum chemical computations. The global minimum energy structures for each cluster are experimentally observed and are characterized by one of the three different S-S⋅⋅⋅H-C/N/O disulfide-centered hydrogen bonds and two O⋅⋅⋅H-C hydrogen bonds. Non-covalent interaction and natural bond orbital analyses further confirm the experimental observations. The symmetry-adapted perturbation theory (SAPT) analysis reveals that electrostatic is dominant in diethyl disulfide⋅⋅⋅H₂ O/HCONH₂ clusters being consistent with normal hydrogen bonds, whilst dispersion takes over in diethyl disulfide⋅⋅⋅H₂ CO cluster. Our study gives accurate structural parameters for the disulfide bond involved non-covalent clusters providing important benchmarking data for the theoretical evaluation of more complex systems.

Phosphorescent MoS2 quantum dots as a temperature sensor and security ink

Currently, few phosphorescent materials (PMs) possess a long phosphorescence lasting time and have potential for application in chemical sensors. Herein, we disclose that the incorporation of few-layer molybdenum disulfide quantum dots (FL-MoS2 QDs) into poly(vinyl alcohol) (PVA) matrices leads to the emission of bright green phosphorescence with a long lasting time of 3.0 s and a phosphorescence quantum yield of 20%. This enhanced phosphorescence originates from the formation of O-H⋯S hydrogen bonding networks between the rich sulfur sites of the FL-MoS2 QDs and the hydroxyl groups of the PVA molecules, which not only rigidifies the vibration modes of the FL-MoS2 QDs but also provides an oxygen barrier. Further investigations reveal that the FL-MoS2 QD/PVA composites exhibit a longer phosphorescence lasting time than N,S-doped carbon dots, few layer tungsten disulfide quantum dots, Rhodamine 6G, and Rhodamine B in PVA matrices. Since heat efficiently induced the removal of water moisture from PVA matrices, the FL-MoS2 QD/PVA composites could be implemented for phosphorescence turn-on and naked-eye detection of temperature variations ranging from 30 to 70 °C. By contrast, the carbon dot/PVA composites were incapable of sensing environmental temperature due to their weak hydrogen bonding with the hydroxyl groups of PVA matrices. Additionally, this study reveals the potential of the FL-MoS2 QD/PVA composites as an advanced security ink for anti-counterfeiting and encryption applications. The given results could open a new direction for potential application of two-dimensional quantum dots in phosphorescence-based sensors and security inks.

Long-chain polyamide covalent adaptable networks based on renewable ethylene brassylate and disulfide exchange

Long-chain polyamide covalent adaptable networks with high strength and short relaxation times were prepared based on a renewable ethylene brassylate and disulfide exchange.

Origins of the Increased Affinity of Phosphorothioate-Modified Therapeutic Nucleic Acids for Proteins

The phosphorothioate backbone modification (PS) is one of the most widely used chemical modifications for enhancing the drug-like properties of nucleic acid-based drugs, including antisense oligonucleotides (ASOs). PS-modified nucleic acid therapeutics show improved metabolic stability from nuclease-mediated degradation and exhibit enhanced interactions with plasma, cell-surface, and intracellular proteins, which facilitates their tissue distribution and cellular uptake in animals. However, little is known about the structural basis of the interactions of PS nucleic acids with proteins. Here, we report a crystal structure of the DNA-binding domain of a model ASO-binding protein PC4, in complex with a full PS 2'-OMe DNA gapmer ASO. To our knowledge this is the first structure of a complex between a protein and fully PS nucleic acid. Each PC4 dimer comprises two DNA-binding interfaces. In the structure one interface binds the 5'-terminal 2'-OMe PS flank of the ASO, while the other interface binds the regular PS DNA central part in the opposite polarity. As a result, the ASO forms a hairpin-like structure. ASO binding also induces the formation of a dimer of dimers of PC4, which is stabilized by base pairing between homologous regions of the ASOs bound by each dimer of PC4. The protein interacts with the PS nucleic acid through a network of electrostatic and hydrophobic interactions, which provides insights into the origins for the enhanced affinity of PS for proteins. The importance of these contacts was further confirmed in a NanoBRET binding assay using a Nano luciferase tagged PC4 acting as the BRET donor, to a fluorescently conjugated ASO acting as the BRET acceptor. Overall, our results provide insights into the molecular forces that govern the interactions of PS ASOs with cellular proteins and provide a potential model for how these interactions can template protein-protein interactions causative of cellular toxicity.

Cis/Trans Energetics in Epoxide, Thiirane, Aziridine and Phosphirane Containing Cyclopentanols: Effects of Intramolecular OH⋯O, S, N and P Contacts

A recent computational analysis of the stabilizing intramolecular OH⋯O contact in 1,2-dialkyl-2,3-epoxycyclopentanol diastereomers has been extended to thiiriane, aziridine and phosphirane analogues. Density functional theory (DFT), second-order Møller-Plesset perturbation theory (MP2) and CCSD(T) coupled-cluster computations with simple methyl and ethyl substituents indicate that electronic energies of the cis isomers are lowered by roughly 3 to 4 kcal mol⁻¹ when the OH group of these cyclopentanol systems forms an intramolecular contact with the O, S, N or P atom on the adjacent carbon. The results also suggest that S and P can participate in these stabilizing intramolecular interactions as effectively as O and N in constrained molecular environments. The stabilizing intramolecular OH⋯O, OH⋯S, OH⋯N and OH⋯P contacts also increase the covalent OH bond length and significantly decrease the OH stretching vibrational frequency in every system with shifts typically on the order of −41 cm⁻¹.

FTIR study of hydrogen bonding interaction between fluorinated alcohol and unsaturated esters

The 1:1 complexes of two unsaturated esters with 2,2,2-trifluoroethanol (TFE) were investigated experimentally and computationally. The experimental observations of the spectral shifts of the OH-stretching vibrational transitions were obtained at 113cm^-1 for TFE-methyl acrylate (MA) and 92cm^-1 for TFE-vinyl acetate (VA). There are three docking sites in the two unsaturated esters for the incoming TFE. The predicted red shifts of the OH-stretching vibrational transitions were found to be larger for the OH⋯OC hydrogen bonded conformer than those for the OH⋯π and OH⋯O ones. The binding energies further prove that the OH⋯OC hydrogen bonded conformers are the most stable ones. On the basis of the DFT calculations as well as previous works, the carbonyl group is the best docking site for TFE. Furthermore, the thermodynamic equilibrium constants of TFE-MA and TFE-VA were obtained at 0.28 and 0.15 by combining the experimental spectra data and the DFT calculations. Consequently, the Gibbs free energies of formation were determined to be 3.2 and 4.8kJmol^-1 for TFE-MA and TFE-VA, respectively. The quantum theory of atoms in molecules (AIM) and generalized Kohn-Sham energy decomposition analysis (GKS-EDA) were carried out for further characterization of the hydrogen bonding interactions. GKS-EDA shows an "electrostatic" dominated hydrogen bonding character for the OH⋯OC hydrogen bonds.

Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy

The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe-S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe-S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. The 4 kcal/mol is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.

Correlations and statistical analysis of solvent molecule hydrogen bonding – a case study of dimethyl sulfoxide (DMSO)

A statistical study of the correlation between predicted solubility of DMSO solvates and hydrogen bonds between solvent and host molecules.

The Influence of the Position of the Double Bond and Ring Size on the Stability of Hydrogen Bonded Complexes

To study the influence of the position of the double bond and ring size on the stability of hydrogen bonded complexes, the 1:1 complexes formed between 2,2,2-trifluoroethanol (TFE) and three heterocyclic compounds including 2,3-dihydrofuran (2,3-DHF), 2,5-dihydrofuran (2,5-DHF) and 3,4-dihydropyran (3,4-DHP) were investigated systematically. The formation of hydrogen bonded TFE−2,3-DHF, TFE−2,5-DHF and TFE−3,4-DHP complexes were identified by gas phase FTIR spectroscopy at room temperature, and the OH-stretching fundamental transition of TFE was red shifted upon complexation. The competition between the O atom and π-electrons bonding sites within the complexes was studied, and the O−H···π type hydrogen bond was found to be less stable than the O−H···O in all three cases. The observed red shifts of the OH-stretching fundamental transitions in the complexes were attributed to the formation of O−H···O hydrogen bond. Equilibrium constants of the complexation reactions were determined from measured and calculated OH-stretching fundamental intensities. Both theoretical calculations and experimental results reveal that the hydrogen bond strengths in the complexes follow the sequence: TFE−2,5-DHF > TFE−2,3-DHF ≈ TFE−3,4-DHP, thus the position of the double bond exerts significantly larger influence than ring size on the stability of the selected hydrogen bonded complexes.

Hydrogen bond docking site competition in methyl esters

The OH⋯O hydrogen bonds in the 2,2,2-trifluoroethanol (TFE)-methyl ester complexes in the gas phase have been investigated by FTIR spectroscopy and DFT calculations. Methyl formate (MF), methyl acetate (MA), and methyl trifluoroacetate (MTFA) were chosen as the hydrogen bond acceptors. A dominant inter-molecular hydrogen bond was formed between the OH group of TFE and different docking sites in the methyl esters (carbonyl oxygen or ester oxygen). The competition of the two docking sites decides the structure and spectral properties of the complexes. On the basis of the observed red shifts of the OH-stretching transition with respect to the TFE monomer, the order of the hydrogen bond strength can be sorted as TFE-MA (119cm^-1)>TFE-MF (93cm^-1)>TFE-MTFA (44cm^-1). Combining the experimental infrared spectra with the DFT calculations, the Gibbs free energies of formation were determined to be 1.5, 4.5 and 8.6kJmol^-1 for TFE-MA, TFE-MF and TFE-MTFA, respectively. The hydrogen bonding in the MTFA complex is much weaker than those of the TFE-MA and TFE-MF complexes due to the effect of the CF₃ substitution on MTFA, while the replacement of an H atom with a CH₃ group in methyl ester only slightly increases the hydrogen bond strength. Topological analysis and localized molecular orbital energy decomposition analysis was also applied to compare the interactions in the complexes.

Contribution of methane sulfonic acid to new particle formation in the atmosphere

Methane sulfonic acid (MSA) is present in substantial concentrations in the gas phase over oceans and coastal regions. We present an investigation into the contribution of MSA to new particle formation with the common atmospheric aerosol nucleation precursors including MSA, methanol, formic acid, acetone, dimethylether, formaldehyde, methyl formate, by making use a quantum chemical approach. Density functional theory calculations indicate that these bimolecular complexes are characterized by the presence of strong inter-molecular hydrogen bonds (SOH⋯O) with large binding energies and thermodynamic equilibrium constants. Topological analysis employing quantum theory of atoms in molecules shows that the charge density of the SOH⋯O hydrogen bonds of the MSA complexes falls in the range of hydrogen bonding criteria, but the Laplacian at bond critical points exceeds the range, which is due to the strong hydrogen bonding interactions. In all the studied complexes, the electrostatic interactions are found to be the main attractive force by localized molecular orbital energy decomposition analysis. All these indicate the environmental fate of MSA could play the role of nucleation centers in new particle formation. The effect of the atmospheric heights (0-12 km) was also considered. The Gibbs free energy of formation decreases with the increase of the atmospheric height owing to the decrease of the atmospheric temperature and pressure. The calculated Gibbs free energies of formation within the atmospheric temperature and pressure range could help to understand the atmospheric pollution.

Matrix isolation FTIR study of hydrogen-bonded complexes of methanol with heterocyclic organic compounds

Hydrogen bonded complexes of heterocyclic compounds with methanol were studied using matrix isolation FTIR spectroscopy and theoretical calculations.

Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol

Amides are important atmospheric organic–nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N-methylformamide, N,N-dimethylformamide, acetamide, N-methylacetamide and N,N-dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH–amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O–H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components.

Acid-Base Formalism Extended to Excited State for O-H···S Hydrogen Bonding Interaction

Hydrogen bond can be regarded as an interaction between a base and a proton covalently bound to another base. In this context the strength of hydrogen bond scales with the proton affinity of the acceptor base and the pKa of the donor, i.e., it follows the acid-base formalism. This has been amply demonstrated in conventional hydrogen bonds. Is this also true for the unconventional hydrogen bonds involving lesser electronegative elements such as sulfur atom? In our previous work, we had established that the strength of O-H···S hydrogen bonding (HB) interaction scales with the proton affinity (PA) of the acceptor. In this work, we have investigated the other counterpart, i.e., the H-bonding interaction between the photoacids with different pKa values with a common base such as the H2O and H2S. The 1:1 complexes of five para substituted phenols p-aminophenol, p-cresol, p-fluorophenol, p-chlorophenol, and p-cyanophenol with H2O and H2S were investigated experimentally and computationally. The investigations were also extended to the excited states. The experimental observations of the spectral shifts in the O-H stretching frequency and the S1-S0 band origins were correlated with the pKa of the donors. Ab initio calculations at the MP2 and various dispersion corrected density functional levels of theory were performed to compute the dissociation energy (D0) of the complexes. The quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI) method, natural bonding orbital (NBO) analysis, and natural decomposition analysis (NEDA) were carried out for further characterization of HB interaction. The O-H stretching frequency red shifts and the dissociation energies were found to be lower for the O-H···S hydrogen bonded systems compared to those for the O-H···O H-bound systems. Despite being dominated by the dispersion interaction the O-H···S interaction in the H2S complexes also conformed to the acid-base formalism, i.e., the D0 and the O-H red shift scaled with the pKa of the donor, similar to that observed in the O-H···O interaction. However, the two classes of H-bonds follow different correlations. In addition we also discuss the nuances associated with the similarity and differences in the hydrogen bonding properties of the two classes in the ground electronic state as well as in the excited state.

Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity

Oxygen-to-sulfur substitutions in DNA phosphate often enhance affinity for DNA-binding proteins. Our previous studies have suggested that this effect of sulfur substitution of both OP1 and OP2 atoms is due to an entropic gain associated with enhanced ion pair dynamics. In this work, we studied stereospecific effects of single sulfur substitution of either the OP1 or OP2 atom in DNA phosphate at the Lys57 interaction site of the Antennapedia homeodomain-DNA complex. Using crystallography, we obtained structural information on the RP and SP diastereomers of the phosphoromonothioate and their interaction with Lys57. Using fluorescence-based assays, we found significant affinity enhancement upon sulfur substitution of the OP2 atom. Using NMR spectroscopy, we found significant mobilization of the Lys57 side-chain NH3 (+) group upon sulfur substitution of the OP2 atom. These data provide further mechanistic insights into the affinity enhancement by oxygen-to-sulfur substitution in DNA phosphate.

Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate

Dithioation of DNA phosphate is known to enhance binding affinities, at least for some proteins. We mechanistically characterized this phenomenon for the Antennapedia homeodomain-DNA complex by integrated use of fluorescence, isothermal titration calorimetry, NMR spectroscopy, and x-ray crystallography. By fluorescence and isothermal titration calorimetry, we found that this affinity enhancement is entropy driven. By NMR, we investigated the ionic hydrogen bonds and internal motions of lysine side-chain NH3(+) groups involved in ion pairs with DNA. By x-ray crystallography, we compared the structures of the complexes with and without dithioation of the phosphate. Our NMR and x-ray data show that the lysine side chain in contact with the DNA phosphate becomes more dynamic upon dithioation. Our thermodynamic, structural, and dynamic investigations collectively suggest that the affinity enhancement by the oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic gain arising from mobilization of the intermolecular ion pair at the protein-DNA interface.

NMR studies on the dynamics of hydrogen bonds and ion pairs involving lysine side chains of proteins

Hydrogen bonds and ion pairs involving side chains play vital roles in protein functions such as molecular recognition and catalysis. Despite the wealth of structural information about hydrogen bonds and ion pairs at functionally crucial sites on proteins, the dynamics of these fundamental chemical interactions are not well understood largely due to the lack of suitable experimental tools in the past. NMR spectroscopy is a powerful tool for investigations of protein dynamics, but the vast majority of NMR methods had been applicable only to the backbone or methyl groups. Recently, a substantial progress has been made in the research on the dynamics of hydrogen bonds and ion pairs involving lysine side-chain NH3+ groups. Together with computational/theoretical approaches, the new NMR methods provide unique insights into the dynamics of hydrogen bonds and ion pairs involving lysine side chains. Here, the methodology and its applications are reviewed.

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning

Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme.

Accurate thermodynamic properties of gas phase hydrogen bonded complexes

The increase in temperature causes a decrease in equilibrium constant, which makes accurate determination of the enthalpy of complex formation possible.

Hydrogen bonding in alcohol–ethylene oxide and alcohol–ethylene sulfide complexes

The O–H⋯O and O–H⋯S hydrogen bonds are of similar strength in the corresponding alcohol–EO and alcohol–ES complexes.

Hydrogen bonding in cyclic complexes of carboxylic acid–sulfuric acid and their atmospheric implications

Carboxylic acids form cyclic ring structures with sulfuric acid and they could potentially be important in new particle formation.