Correlations of NHN hydrogen bond energy with geometry and 1H NMR chemical shift difference of NH protons for aniline complexes

Probing London Dispersion in Proton-Bound Onium Ions: Are Alkyl-Alkyl Steric Interactions Reliably Modeled?

We report spectroscopic and spectrometric experiments that probe the London dispersion interaction between tert-butyl substituents in three series of covalently linked, protonated bis-pyridines in the gas phase. Molecular ions in the three test series, along with several reference molecules for control, were electrosprayed from solution into the gas phase and then probed by infrared multiphoton dissociation spectroscopy and trapped ion mobility spectrometry. The observed N-H stretching frequencies provided an experimental readout diagnostic of the ground-state geometry of each ion, which could be furthermore compared to a second, independent structural readout via the collision cross section. In each of the three series, the strength of a London dispersion interaction could be modulated systematically by a progressive increase in the size of substituents from H to Me to tert-Bu. Parallel to the experimental study, extensive dispersion-corrected density functional theory (DFT-D3BJ) calculations were performed with a range of exchange correlation functionals. A full analysis of the conformational space for the flexible members of the series, and an analysis of the vibrational spectra in the context of a general double-well potential, finds that DFT-D3BJ appears to significantly overbind alkyl-alkyl interactions, specifically interactions between tert-Bu groups, even failing to predict the minimum energy structures reliably in the case of molecules in which London dispersion competes with other noncovalent interactions such as hydrogen bonding.

Twin hydrogen bonds with phosphine oxide: anticooperativity effects caused by competing proton donors

In this computational work we study complexes with two equivalent intermolecular hydrogen bonds formed between trimethyl phosphine oxide and two identical proton donors ("twin" hydrogen bonds) for a set of 70 proton donor molecules. The changes in the phosphorus chemical shift and stretching frequency of the PO group upon complexation correlate quite well with the total strength of two hydrogen bonds. A set of explicit numerical dependences is proposed for assessing interatomic distances and hydrogen bond strengths from spectral data. Comparison with the results obtained for analogous previously studied 1 : 1 complexes allowed us to analyze in detail anticooperativity effects on the geometry, energy and spectral parameters. Two hydrogen bonds compete for the PO acceptor group and their mutual weakening increases nonlinearly with the strengthening of the complex, reaching approximately 25% in energy (which corresponds to 0.1 Å lengthening for short strong H-bonds), which is clearly seen in NMR and IR spectra and correlates well with the changes in the spectral parameters.

Synthesis and characterization of a nanostructure conductive copolymer based on polyaniline and polylactic acid as an effective substrate in proteins impedimetric biosensing

Despite of all the developments in DNA microarray technology, there is not sufficient knowledge about protein abundance or their function in processes such as proteolysis, phosphorylation. Therefore, there is a significant need for direct detection and quantification of proteins, especially in processes such as proteomics, drug design and disease prediction. The present work introduce the new generation of polymeric substrate based on polyaniline and, polylactic acid, which it was used for impedimetric sensor in detection of proteins in particular for bovine serum albumin (BSA). In this copolymerization, the polylactic acid-block-polyaniline copolymer (PLA-b-PANI) was synthesized to attach polylactic acid and polyaniline using epichlorohydrin as a coupling agent. The structure of synthesized compounds in all steps, were confirmed by FT-IR and, 1H-NMR. The thermal properties and, morphology were analyzed by DSC, TGA, and, SEM. Also the electrochemical characteristics of fabricated PLA-b-PANI electrode were investigated by Electrochemical Impedance Spectroscopy (EIS) and Cyclic Voltammetry (CV). The results demonstrated that morphology of the PLA-b-PANI is sphere shape nanoparticles with dimension less than 100 nanometer diameters and, reasonable thermal properties. PLA-b-PANI was used to modify a screen-printed carbon electrode (SPCE) to fabricate a BSA impedimetric sensor. In order to increase the performance of the proposed impedimetric sensor, optimization of incubation time, pH and amount of PLA-b-PANI were investigated. The results show that the impedimetric sensor has the highest response when the electrode surface is covered with 5 microliters of PLA-b-PANI, and is incubated in BSA solution with pH 6.5 for 5 min. Impedimetric results showed that the PLA-b-PANI has excellent properties in reducing the charge transfer resistance and increasing the electron charge transfer rate. The final impedimetric sensor exhibited good repeatability, reproducibility, and chemical stability within the linear concentration range of 0.1-20 μg L-1 of BSA, and a detection limit of 0.05 μg L-1.

Evolution of vibrational bands upon gradual protonation/deprotonation of arsinic acid H2As(O)OH in media of different polarity

This computational work is devoted to the investigation (MP2/def2-TZVP) of the geometry and IR parameters of arsinic acid H₂AsOOH and its hydrogen-bonded complexes under vacuum and in media with different polarity. The medium effects were accounted for in two ways: (1) implicitly, using the IEFPCM model, varying the dielectric permittivity (ε) and (2) explicitly, by considering hydrogen-bonded complexes of H₂As(O)OH with various hydrogen bond donors (41 complexes) or acceptors (38 complexes), imitating a gradual transition to the As(OH)₂⁺ or AsO₂^- moiety, respectively. It was shown that the transition from vacuum to a medium with ε > 1 causes the As(O)OH fragment to lose its flatness. The solvent polar medium introduces significant changes in the geometry and IR spectral parameters of hydrogen-bonded complexes too: as the polarity of a medium increases, weak hydrogen bonds become weaker, and strong and medium hydrogen bonds become stronger; in the case of a complex with two hydrogen bonds cooperativity effects are observed. In almost all cases the driving force of these changes appears to be preferential solvation of charge-separated structures. In the limiting case of complete deprotonation (or conversely complete protonation) the vibrational frequencies of ν_AsO and ν_As-O turn into ν_As-O(asym) and ν_As-O(sym), respectively. In the intermediate cases the distance between ν_AsO and ν_As-O is sensitive to both implicit solvation and explicit solvation and the systematic changes of this distance can be used for estimation of the degree of proton transfer within the hydrogen bond.

Estimations of OH·N hydrogen bond length from positions and intensities of IR bands

In this computational work applicability of IR spectral parameters for evaluations of OH···N hydrogen bond length is discussed. For a set of 124 complexes with OH···N hydrogen bond formed by combinations of methanol/acetic acid and pyridine (and their fluorine substituted versions) geometries, energies and IR parameters were calculated at MP2/def2-TZVP level of theory. For a number of IR parameters (the shift of proton donor group stretching vibration Δν_s, increase of its intensity I, the low-frequency hydrogen bond stretching vibration ν_σ, bending in-plane δ and out-of-plane γ vibrations) equations linking them with interatomic distances are proposed, the robustness and accuracy of such equations are discussed. The enthalpy of OH···N hydrogen bond formation ΔH was also linked with electron density parameters in (3; -1) critical point.

Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems

With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.

Phosphine oxides as NMR and IR spectroscopic probes for geometry and energy of PO···H–A hydrogen bonds

In this work we evaluate the possibility to use the NMR and IR spectral properties of P=O group to estimate the geometry and strength of hydrogen bonds which it forms...

Pore-Bound Water at the Key Residue Histidine 37 in Influenza A M2

Atomic details of structured water molecules are indispensable to understand the thermodynamics of important biological processes including the proton conduction mechanism of the M2 protein. Despite the expectation of structured water molecules based on crystal structures of Influenza A M2, only two water populations have been observed by NMR in reconstituted lipid bilayer samples. These are the bulk‐ and lipid‐associated water populations typically seen in membrane samples. Here, we detect a bound water molecule at a chemical shift of 11 ppm, located near the functional histidine 37 residue in the M2 conductance domain, which comprises residues 18 to 60. Combining 100 kHz magic‐angle spinning NMR, dynamic nuclear polarization and density functional theory calculations, we show that the bound water forms a hydrogen bond to the δ1 nitrogen of histidine 37.

Modeling of the Response of Hydrogen Bond Properties on an External Electric Field: Geometry, NMR Chemical Shift, Spin-Spin Scalar Coupling

The response of the geometric and NMR properties of molecular systems to an external electric field has been studied theoretically in a wide field range. It has been shown that this adduct under field approach can be used to model the geometric and spectral changes experienced by molecular systems in polar media if the system in question has one and only one bond, the polarizability of which significantly exceeds the polarizability of other bonds. If this requirement is met, then it becomes possible to model even extreme cases, for example, proton dissociation in hydrogen halides. This requirement is fulfilled for many complexes with one hydrogen bond. For such complexes, this approach can be used to facilitate a detailed analysis of spectral changes associated with geometric changes in the hydrogen bond. For example, in hydrogen-bonded complexes of isocyanide C≡¹⁵N-¹H⋯X, ¹J(¹⁵N¹H) depends exclusively on the N-H distance, while δ(¹⁵N) is also slightly influenced by the nature of X.

Classification of So-Called Non-Covalent Interactions Based on VSEPR Model

The variety of interactions have been analyzed in numerous studies. They are often compared with the hydrogen bond that is crucial in numerous chemical and biological processes. One can mention such interactions as the halogen bond, pnicogen bond, and others that may be classified as σ-hole bonds. However, not only σ-holes may act as Lewis acid centers. Numerous species are characterized by the occurrence of π-holes, which also may play a role of the electron acceptor. The situation is complicated since numerous interactions, such as the pnicogen bond or the chalcogen bond, for example, may be classified as a σ-hole bond or π-hole bond; it ultimately depends on the configuration at the Lewis acid centre. The disadvantage of classifications of interactions is also connected with their names, derived from the names of groups such as halogen and tetrel bonds or from single elements such as hydrogen and carbon bonds. The chaos is aggravated by the properties of elements. For example, a hydrogen atom can act as the Lewis acid or as the Lewis base site if it is positively or negatively charged, respectively. Hence names of the corresponding interactions occur in literature, namely hydrogen bonds and hydride bonds. There are other numerous disadvantages connected with classifications and names of interactions; these are discussed in this study. Several studies show that the majority of interactions are ruled by the same mechanisms related to the electron charge shifts, and that the occurrence of numerous interactions leads to specific changes in geometries of interacting species. These changes follow the rules of the valence-shell electron-pair repulsion model (VSEPR). That is why the simple classification of interactions based on VSEPR is proposed here. This classification is still open since numerous processes and interactions not discussed in this study may be included within it.

Strategic engineering of alkyl spacer length for a pH-tolerant lysosome marker and dual organelle localization

Long-term visualization of lysosomal properties is extremely crucial to evaluate diseases related to their dysfunction. However, many of the reported lysotrackers are less conducive to imaging lysosomes precisely because they suffer from fluorescence quenching and other inherent drawbacks such as pH-sensitivity, polarity insensitivity, water insolubility, slow diffusibility, and poor photostability. To overcome these limitations, we have utilized an alkyl chain length engineering strategy and synthesized a series of lysosome targeting fluorescent derivatives namely NIMCs by attaching a morpholine moiety at the peri position of the 1,8-naphthalimide (NI) ring through varying alkyl spacers between morpholine and 1,8-naphthalimide. The structural and optical properties of the synthesized NIMCs were explored by 1H-NMR, single-crystal X-ray diffraction, UV-Vis, and fluorescence spectroscopy. Afterward, optical spectroscopic measurements were carefully performed to identify a pH-tolerant, polarity sensitive, and highly photostable fluoroprobes for further live-cell imaging applications. NIMC6 displayed excellent pH-tolerant and polarity-sensitive properties. Consequently, all NIMCs were employed in kidney fibroblast cells (BHK-21) to investigate their applicability for lysosome targeting and probing lysosomal micropolarity. Interestingly, a switching of localization from lysosomes to the endoplasmic reticulum (ER) was also achieved by controlling the linker length and this phenomenon was subsequently applied in determining ER micropolarity. Additionally, the selected probe NIMC6 was also employed in BHK-21 cells for 3-D spheroid imaging and in Caenorhabditis elegans (C. elegans) for in vivo imaging, to evaluate its efficacy for imaging animal models.

A Spectroscopic Overview of Intramolecular Hydrogen Bonds of NH…O,S,N Type

Intramolecular NH…O,S,N interactions in non-tautomeric systems are reviewed in a broad range of compounds covering a variety of NH donors and hydrogen bond acceptors. 1H chemical shifts of NH donors are good tools to study intramolecular hydrogen bonding. However in some cases they have to be corrected for ring current effects. Deuterium isotope effects on 13C and 15N chemical shifts and primary isotope effects are usually used to judge the strength of hydrogen bonds. Primary isotope effects are investigated in a new range of magnitudes. Isotope ratios of NH stretching frequencies, νNH/ND, are revisited. Hydrogen bond energies are reviewed and two-bond deuterium isotope effects on 13C chemical shifts are investigated as a possible means of estimating hydrogen bond energies.

Estimations of FH···X hydrogen bond energies from IR intensities: Iogansen's rule revisited

In this work the possibility of using the IR intensity of the stretching vibration ν_s of proton donor group for estimation of hydrogen bond strength was investigated. For a set of complexes with FH···X (X = F, N, O) hydrogen bonds in the wide range of energies (0.1-49.2 kcal/mol) vibrational frequencies ν_s and their intensities A were calculated (CCSD at complete basis set limit). The validity of the previously proposed linear proportionality between the intensification of the stretching vibration ν_s in IR spectra and hydrogen bond enthalpy -ΔH = 12.2 ∆ A (A. V. Iogansen, Spectrochimica Acta A 1999) was examined. It is shown that for a range of similar hydrogen bond types with complexation energies ∆E <15 kcal/mol the ∆E( ∆ A ) function remains similar to that proposed in the Iogansen's work, while upon strengthening this dependency becomes significantly nonlinear. We examined two other parameters ( ∆ A ν s and ∆ A ∙ m R ) related to IR intensity as descriptors of hydrogen bond strength which are proportional to transition dipole moment matrix element and mass-independent dipole moment derivative. It was found that the dependency ∆E( ∆ A ν s ) stays linear in the whole studied range of complexation energies and it can be used for evaluation of ∆E from infrared spectral data with the accuracy about 2 kcal/mol. The mass-independent product ∆ A ∙ m R is an appropriate descriptor for sets of complexes with various hydrogen bond types. Simple equations proposed in this work can be used for estimations of hydrogen bond strength in various systems, where experimental thermodynamic methods or direct calculations are difficult or even impossible.

Self-Assembly of Hydrogen-Bonded Cage Tetramers of Phosphonic Acid

The self-association of phosphonic acids with general formula RP(O)(OH)2 in solution state remains largely unexplored. The general understanding is that such molecules form multiple intermolecular hydrogen bonds, but the stoichiometry of self-associates and the bonding motifs are unclear. In this work, we report the results of the study of self-association of tert-butylphosphonic acid using low temperature liquid-state 1H and 31P NMR spectroscopy (100 K; CDF3/CDF2Cl) and density functional theory (DFT) calculations. For the first time, we demonstrate conclusively that polar aprotic medium tert-butylphosphonic acid forms highly symmetric cage-like tetramers held by eight OHO hydrogen bonds, which makes the complex quite stable. In these associates. each phosphonic acid molecule is bonded to three other molecules by forming two hydrogen bonds as proton donor and two hydrogen bonds as proton acceptor. Though the structure of such cage-like tetramers is close to tetrahedral, the formal symmetry of the self-associate is C2.

Intramolecular Hydrogen Bond Energy and Its Decomposition—O–H∙∙∙O Interactions

The method to calculate the energy of intramolecular hydrogen bond is proposed and tested for a sample of malonaldehyde and its fluorine derivatives; the corresponding calculations were performed at the ωB97XD/aug-cc-pVTZ level. This method based on relationships found for related intermolecular hydrogen bonds is compared with other approaches which may be applied to estimate the intramolecular hydrogen bond energy. Particularly, methods based on the comparison of the system that contains the intramolecular hydrogen bond compared with corresponding conformations where such interaction does not occur are discussed. The function-based energy decomposition analysis, FB-EDA, of the intramolecular hydrogen bonds is also proposed here.

Stretching force constants as descriptors of energy and geometry of F···HF hydrogen bonds

In this work applicability of proton donor group stretching vibration force constants k_s and intermolecular stretching force constants k_σ for evaluations of hydrogen bond strength and geometry are discussed. For a set of 30 complexes with F···HF hydrogen bonds in a wide range 0.5-48 kcal/mol by means of quantum chemical calculations equilibrium geometries, complexation energies, vibrational frequencies and corresponding force constants were calculated (MP2/aug-cc-pVTZ). It is shown, that properties of a hydrogen bond are more strictly correlated with the values of force constants than with vibrational frequencies. Easy-to-use equations for estimations of hydrogen bond energy ∆E and geometry (r_FH, r_FF) based on k_s and k_σ values are proposed.

H/D Isotope Effects on 1H-NMR Chemical Shifts in Cyclic Heterodimers and Heterotrimers of Phosphinic and Phosphoric Acids

Hydrogen-bonded heterocomplexes formed by POOH-containing acids (diphenylphosphoric 1, dimethylphosphoric 2, diphenylphosphinic 3, and dimethylphosphinic 4) are studied by the low-temperature (100 K) ¹H-NMR and ³¹P-NMR using liquefied gases CDF₃/CDF₂Cl as a solvent. Formation of cyclic dimers and cyclic trimers consisting of molecules of two different acids is confirmed by the analysis of vicinal H/D isotope effects (changes in the bridging proton chemical shift, δH, after the deuteration of a neighboring H-bond). Acids 1 and 4 (or 1 and 3) form heterotrimers with very strong (short) H-bonds (δH ca. 17 ppm). While in the case of all heterotrimers the H-bonds are cyclically arranged head-to-tail, ···O=P-O-H···O=P-O-H···, and thus their cooperative coupling is expected, the signs of vicinal H/D isotope effects indicate an effective anticooperativity, presumably due to steric factors: when one of the H-bonds is elongated upon deuteration, the structure of the heterotrimer adjusts by shortening the neighboring hydrogen bonds. We also demonstrate the formation of cyclic tetramers: in the case of acids 1 and 4 the structure has alternating molecules of 1 and 4 in the cycle, while in case of acids 1 and 3 the cycle has two molecules of 1 followed by two molecules of 3.

Quantitative decomposition of resonance-assisted hydrogen bond energy in β-diketones into resonance and hydrogen bonding (π- and σ-) components using molecular tailoring and function-based approaches

Using the molecular tailoring and function-based approaches allows one to divide the energy of the O─H⋯O═C resonance-assisted hydrogen bond in a series of the β-diketones into resonance and hydrogen bonding components. The magnitude of the resonance component is assessed as about 6 kcal mol^-1 . This value increases by ca. 1 kcal mol^-1 on going from the weak to strong resonance-assisted hydrogen bonding. The magnitude of the hydrogen bonding component varies in the wide range from 2 to 20 kcal mol^-1 depending on the structure of the β-diketone in question.

How Strong is Hydrogen Bonding to Amide Nitrogen?

The protonation of the carboxamide nitrogen atom is an essential part of in vivo and in vitro processes (cis-trans isomerization, amides hydrolysis etc). This phenomenon is well studied in geometrically strongly distorted amides, although there is little data concerning the protonation of undistorted amides. In the latter case, the participation of amide nitrogen in hydrogen bonding (which can be regarded as the incipient state of a proton transfer process) is less well-studied. Thus, it would be a worthy goal to investigate the enthalpy of this interaction. We prepared and investigated a set of peri-substituted naphthalenes containing the protonated dimethylamino group next to the amide nitrogen atom ("amide proton sponges"), which could serve as models for the study of an intramolecular hydrogen bond with the amide nitrogen atom. X-Ray analysis, NMR spectra, basicity values as well as quantum chemical calculations revealed the existence of a hydrogen bond with the amide nitrogen, that should be attributed to the borderline between moderate and weak intramolecular hydrogen bonds (2-7 kcal ⋅ mol^-1 ).

Hydrogen peroxide adducts of triarylphosphine oxides

Five new hydrogen peroxide adducts of phosphine oxides (p-Tol₃PO·H₂O₂)₂ (1), (o-Tol₃PO·H₂O₂)₂ (2), (o-Tol₂PhPO·H₂O₂)₂ (3), (p-Tol₃PO)₂·H₂O₂ (4), and (o-TolPh₂PO)₂·H₂O₂ (5), and the water adduct (o-Tol₂PhPO·H₂O)₂ (6) have been synthesized and fully characterized. Their single crystal X-ray structures have been determined and analyzed. The IR and ³¹P NMR data are in accordance with strong hydrogen bonding of the hydrogen peroxide. The mono- versus dimeric nature of the adduct assemblies has been investigated by DOSY NMR experiments. Raman spectroscopy of the symmetric adducts and the ν(O-O) stretching bands confirm the presence of hydrogen-bonded hydrogen peroxide in the solid materials. The solubilities in organic solvents have been quantified. Due to the high solubilities of 1-6 in organic solvents their ¹⁷O NMR spectra could be recorded in natural abundance, providing well-resolved signals for the P[double bond, length as m-dash]O and O-O groups. The adducts 1-5 have been probed regarding their stability in solution at 105 °C. The decomposition of the adduct 1 takes place by loss of the active oxygen atoms in two steps.