Hydrogen/Deuterium Isotope Effects on the NMR Chemical Shifts and Geometries of Intermolecular Low-Barrier Hydrogen-Bonded Complexes

An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts

The majority of primary and secondary metabolites in nature have yet to be identified, representing a major challenge for metabolomics studies that currently require reference libraries from analyses of authentic compounds. Using currently available analytical methods, complete chemical characterization of metabolomes is infeasible for both technical and economic reasons. For example, unambiguous identification of metabolites is limited by the availability of authentic chemical standards, which, for the majority of molecules, do not exist. Computationally predicted or calculated data are a viable solution to expand the currently limited metabolite reference libraries, if such methods are shown to be sufficiently accurate. For example, determining nuclear magnetic resonance (NMR) spectroscopy spectra in silico has shown promise in the identification and delineation of metabolite structures. Many researchers have been taking advantage of density functional theory (DFT), a computationally inexpensive yet reputable method for the prediction of carbon and proton NMR spectra of metabolites. However, such methods are expected to have some error in predicted 13C and 1H NMR spectra with respect to experimentally measured values. This leads us to the question-what accuracy is required in predicted 13C and 1H NMR chemical shifts for confident metabolite identification? Using the set of 11,716 small molecules found in the Human Metabolome Database (HMDB), we simulated both experimental and theoretical NMR chemical shift databases. We investigated the level of accuracy required for identification of metabolites in simulated pure and impure samples by matching predicted chemical shifts to experimental data. We found 90% or more of molecules in simulated pure samples can be successfully identified when errors of 1H and 13C chemical shifts in water are below 0.6 and 7.1 ppm, respectively, and below 0.5 and 4.6 ppm in chloroform solvation, respectively. In simulated complex mixtures, as the complexity of the mixture increased, greater accuracy of the calculated chemical shifts was required, as expected. However, if the number of molecules in the mixture is known, e.g., when NMR is combined with MS and sample complexity is low, the likelihood of confident molecular identification increased by 90%.

An N⋯H⋯N low-barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half-reaction

Pyridoxal 5'-phosphate (PLP)-dependent enzymes have been extensively studied for their ability to fine-tune PLP cofactor electronics to promote a wide array of chemistries. Neutron crystallography offers a straightforward approach to studying the electronic states of PLP and the electrostatics of enzyme active sites, responsible for the reaction specificities, by enabling direct visualization of hydrogen atom positions. Here we report a room-temperature joint X-ray/neutron structure of aspartate aminotransferase (AAT) with pyridoxamine 5'-phosphate (PMP), the cofactor product of the first half reaction catalyzed by the enzyme. Between PMP NSB and catalytic Lys258 Nζ amino groups an equally shared deuterium is observed in an apparent low-barrier hydrogen bond (LBHB). Density functional theory calculations were performed to provide further evidence of this LBHB interaction. The structural arrangement and the juxtaposition of PMP and Lys258, facilitated by the LBHB, suggests active site preorganization for the incoming ketoacid substrate that initiates the second half-reaction.

Transition Metal Catalysis Controlled by Hydrogen Bonding in the Second Coordination Sphere

Transition metal catalysis is of utmost importance for the development of sustainable processes in academia and industry. The activity and selectivity of metal complexes are typically the result of the interplay between ligand and metal properties. As the ligand can be chemically altered, a large research focus has been on ligand development. More recently, it has been recognized that further control over activity and selectivity can be achieved by using the "second coordination sphere", which can be seen as the region beyond the direct coordination sphere of the metal center. Hydrogen bonds appear to be very useful interactions in this context as they typically have sufficient strength and directionality to exert control of the second coordination sphere, yet hydrogen bonds are typically very dynamic, allowing fast turnover. In this review we have highlighted several key features of hydrogen bonding interactions and have summarized the use of hydrogen bonding to program the second coordination sphere. Such control can be achieved by bridging two ligands that are coordinated to a metal center to effectively lead to supramolecular bidentate ligands. In addition, hydrogen bonding can be used to preorganize a substrate that is coordinated to the metal center. Both strategies lead to catalysts with superior properties in a variety of metal catalyzed transformations, including (asymmetric) hydrogenation, hydroformylation, C-H activation, oxidation, radical-type transformations, and photochemical reactions.

A phosphonic acid anion and acid dimer dianion stabilized by proton transfer in OHN hydrogen bonds - models of structural motifs in blend polymer membranes

The structure of intermolecular hydrogen-bonded complexes formed between tert-butylphosphonic acid and trimethylpyridine molecules has been experimentally studied as the simplest model system of the structural motifs in blend proton-conducting polymer membranes based on phosphonic acid residues. The stoichiometry of the formed complexes and proton positions in OHO and OHN hydrogen bonds were established by the H/D isotope effects and temperature dependences of the signals in ¹H and ³¹P NMR spectra. Two structural motifs, namely, 1 : 2 and 2 : 2 acid-base complexes, were identified at the low temperature in a polar aprotic environment. In the 1 : 2 complex, one proton has passed through the hydrogen bond center creating a chain of two cooperatively coupled OHN bonds, while in the 2 : 2 complex both OHN bonds are zwitterionic and anti-cooperatively coupled to each other via a dianionic cyclic dimer of phosphonic acid in the middle. The dianionic cyclic dimer is metastable by itself, but under the used experimental conditions it is stabilized by complexation with two trimethylpyridinium cations. Additionally, quantum chemical calculations using the DFT method were carried out to support the experimental data.

Double Proton Tautomerism via Intra- or Intermolecular Pathways? The Case of Tetramethyl Reductic Acid Studied by Dynamic NMR: Hydrogen Bond Association, Solvent and Kinetic H/D Isotope Effects

Using dynamic liquid-state NMR spectroscopy a degenerate double proton tautomerism was detected in tetramethyl reductic acid (TMRA) dissolved in toluene-d₈ and in CD₂Cl₂. Similar to vitamin C, TMRA belongs to the class of reductones of biologically important compounds. The tautomerism involves an intramolecular HH transfer that interconverts the peripheric and the central positions of the two OH groups. It is slow in the NMR time scale around 200 K and fast at room temperature. Pseudo-first-order rate constants of the HH transfer and of the HD transfer after suitable deuteration were obtained by line shape analyses. Interestingly, the chemical shifts were found to be temperature dependent carrying information about an equilibrium between a hydrogen bonded dimer and a monomer forming two weak intramolecular hydrogen bonds. The structures of the monomer and the dimer are discussed. The latter may consist of several rapidly interconverting hydrogen-bonded associates. A way was found to obtain the enthalpies and entropies of dissociation, which allowed us to convert the pseudo-first-order rate constants of the reaction mixture into first-order rate constants of the tautomerization of the monomer. Surprisingly, these intrinsic rate constants were the same for toluene-d₈ and CD₂Cl₂, but in the latter solvent more monomer is formed. This finding is attributed to the dipole moment of the TMRA monomer, compensated in the dimer, and to the larger dielectric constant of CD₂Cl₂. Within the margin of error, the kinetic HH/HD isotope effects were found to be of the order of 3 but independent of temperature. That finding indicates a stepwise HH transfer involving a tunnel mechanism along a double barrier pathway. The Arrhenius curves were described in terms of the Bell–Limbach tunneling model.

Combined NMR and UV-Vis Spectroscopic Studies of Models for the Hydrogen Bond System in the Active Site of Photoactive Yellow Protein: H-Bond Cooperativity and Medium Effects

Intramolecular hydrogen bonds in aprotic media were studied by combined (simultaneous) NMR and UV-vis spectroscopy. The species under investigation were anionic and featured single or coupled H-bonds between, for example, carboxylic groups and phenolic oxygen atoms (COO···H···OC)^-, among phenolic oxygen atoms (CO···H···OC)^-, and hydrogen bond chains between a carboxylic group and two phenolic oxygen atoms (COO···H···(OC)···H···OC)^-. The last anion may be regarded as a small molecule model for the hydrogen bond system in the active site of wild-type photoactive yellow protein (PYP) while the others mimic the corresponding H-bonds in site-selective mutants. Proton positions in isolated hydrogen bonds and hydrogen bond chains were assessed by calculations for vacuum conditions and spectroscopically for the two media, CD₂Cl₂ and the liquefied gas mixture CDClF₂/CDF₃ at low temperatures. NMR parameters allow for the estimation of time-averaged H-bond geometries, and optical spectra give additional information about geometry distributions. Comparison of the results from the various systems revealed the effects of the formation of hydrogen bond chains and changes of medium conditions on the geometry of individual H-bonds. In particular, the proton in a hydrogen bond to a carboxylic group shifts from the phenolic oxygen atom in the system COO^-···H-OC to the carboxylic group in COO-H···(OC)^-···H-OC as a result of hydrogen bond formation to the additional phenolic donor. Increase in medium polarity may, however, induce the conversion of a structure of a type COO-H···(OC)^-···H-OC to the type COO^-···H-(OC)···H-OC. Application of these results obtained from the model systems to PYP suggests that both cooperative effects within the hydrogen bond chain and a low-polarity protein environment are prerequisites for the stabilization of negative charge on the cofactor and hence for the spectral tuning of the photoreceptor.

The Effect of Deuteration on the H2 Receptor Histamine Binding Profile: A Computational Insight into Modified Hydrogen Bonding Interactions

We used a range of computational techniques to reveal an increased histamine affinity for its H₂ receptor upon deuteration, which was interpreted through altered hydrogen bonding interactions within the receptor and the aqueous environment preceding the binding. Molecular docking identified the area between third and fifth transmembrane α-helices as the likely binding pocket for several histamine poses, with the most favorable binding energy of −7.4 kcal mol⁻¹ closely matching the experimental value of −5.9 kcal mol⁻¹. The subsequent molecular dynamics simulation and MM-GBSA analysis recognized Asp98 as the most dominant residue, accounting for 40% of the total binding energy, established through a persistent hydrogen bonding with the histamine −NH₃⁺ group, the latter further held in place through the N–H∙∙∙O hydrogen bonding with Tyr250. Unlike earlier literature proposals, the important role of Thr190 is not evident in hydrogen bonds through its −OH group, but rather in the C–H∙∙∙π contacts with the imidazole ring, while its former moiety is constantly engaged in the hydrogen bonding with Asp186. Lastly, quantum-chemical calculations within the receptor cluster model and utilizing the empirical quantization of the ionizable X–H bonds (X = N, O, S), supported the deuteration-induced affinity increase, with the calculated difference in the binding free energy of −0.85 kcal mol⁻¹, being in excellent agreement with an experimental value of −0.75 kcal mol⁻¹, thus confirming the relevance of hydrogen bonding for the H₂ receptor activation.

Composition-Dependent Hydrogen-Bonding Motifs and Dynamics in Brønsted Acid-Base Mixtures

In recent years the interaction of organophosphates and imines, which is at the core of Brønsted acid organocatalysis, has been established to be based on strong ionic hydrogen bonds. Yet, besides the formation of homodimers consisting of two acid molecules and heterodimers consisting of one acid and one base, also multimeric molecular aggregates are formed in solution. These multimeric aggregates consist of one base and several acid molecules. The details of the intermolecular bonding in such aggregates, however, have remained elusive. To characterize composition-dependent bonding and bonding dynamics in these aggregates, we use linear and nonlinear infrared (IR) spectroscopy at varying molar ratios of diphenyl phosphoric acid and quinaldine. We identify the individual aggregate species, giving rise to the structured, strong, and very broad infrared absorptions, which span more than 1000 cm^–1. Linear infrared spectra and density functional theory calculations of the proton transfer potential show that doubly ionic intermolecular hydrogen bonds between the acid and the base lead to absorptions which peak at ∼2040 cm^–1. The contribution of singly ionic hydrogen bonds between an acid anion and an acid molecule is observed at higher frequencies. As common to such strong hydrogen bonds, ultrafast IR spectroscopy reveals rapid, ∼ 100 fs, dissipation of energy from the proton transfer coordinate. Yet, the full dissipation of the excess energy occurs on a ∼0.8–1.1 ps time scale, which becomes longer when multimers dominate. Our results thus demonstrate the coupling and collectivity of the hydrogen bonds within these complexes, which enable efficient energy transfer.

The Structure of the "Vibration Hole" around an Isotopic Substitution-Implications for the Calculation of Nuclear Magnetic Resonance (NMR) Isotopic Shifts

Calculations of nuclear magnetic resonance (NMR) isotopic shifts often rest on the unverified assumption that the “vibration hole”, that is, the change of the vibration motif upon an isotopic substitution, is strongly localized around the substitution site. Using our recently developed difference-dedicated (DD) second-order vibrational perturbation theory (VPT2) method, we test this assumption for a variety of molecules. The vibration hole turns out to be well localized in many cases but not in the interesting case where the H/D substitution site is involved in an intra-molecular hydrogen bond. For a series of salicylaldehyde derivatives recently studied by Hansen and co-workers (Molecules2019, 24, 4533), the vibrational hole was found to stretch over the whole hydrogen-bond moiety, including the bonds to the neighbouring C atoms, and to be sensitive to substituent effects. We discuss consequences of this finding for the accurate calculation of NMR isotopic shifts and point out directions for the further improvement of our DD-VPT2 method.

Relevance of Hydrogen Bonds for the Histamine H2 Receptor-Ligand Interactions: A Lesson from Deuteration

We used a combination of density functional theory (DFT) calculations and the implicit quantization of the acidic N–H and O–H bonds to assess the effect of deuteration on the binding of agonists (2-methylhistamine and 4-methylhistamine) and antagonists (cimetidine and famotidine) to the histamine H2 receptor. The results show that deuteration significantly increases the affinity for 4-methylhistamine and reduces it for 2-methylhistamine, while leaving it unchanged for both antagonists, which is found in excellent agreement with experiments. The revealed trends are interpreted in the light of the altered strength of the hydrogen bonding upon deuteration, known as the Ubbelohde effect, which affects ligand interactions with both active sites residues and solvent molecules preceding the binding, thus providing strong evidence for the relevance of hydrogen bonding for this process. In addition, computations further underline an important role of the Tyr250 residue for the binding. The obtained insight is relevant for the therapy in the context of (per)deuterated drugs that are expected to enter therapeutic practice in the near future, while this approach may contribute towards understanding receptor activation and its discrimination between agonists and antagonists.

Efficient calculation of NMR isotopic shifts: Difference-dedicated vibrational perturbation theory

We present difference-dedicated second-order vibrational perturbation theory (VPT2) as an efficient method for the computation of nuclear magnetic resonance (NMR) isotopic shifts, which reflect the geometry dependence of the NMR property in combination with different vibration patterns of two isotopologues. Conventional calculations of isotopic shifts, e.g., by standard VPT2, require scanning the geometry dependence over the whole molecule, which becomes expensive rapidly as the molecule size increases. In DD-VPT2, this scan can be restricted to a small region around the substitution site. At the heart of DD-VPT2 is a set of localized vibration modes common to the two isotopologues and designed such that the difference between the vibration patterns is caught by a small subset of them (usually fewer than 10). We tested the DD-VPT2 method for a series of molecules with increasing size and found that this method provides results with the same quality as VPT2 and in good agreement with the experiment, with computational savings up to 95% and less numerical instabilities. The method is easy to automatize and straightforward to generalize to other molecular properties.

Solvent-independent determination of heteroatom protonation states from NMR spectra by differential deuterium isotope shifts

We present a simple and broadly applicable method to determine the protonation state of heteroatoms in organic compounds.

An automated framework for NMR chemical shift calculations of small organic molecules

When using nuclear magnetic resonance (NMR) to assist in chemical identification in complex samples, researchers commonly rely on databases for chemical shift spectra. However, authentic standards are typically depended upon to build libraries experimentally. Considering complex biological samples, such as blood and soil, the entirety of NMR spectra required for all possible compounds would be infeasible to ascertain due to limitations of available standards and experimental processing time. As an alternative, we introduce the in silico Chemical Library Engine (ISiCLE) NMR chemical shift module to accurately and automatically calculate NMR chemical shifts of small organic molecules through use of quantum chemical calculations. ISiCLE performs density functional theory (DFT)-based calculations for predicting chemical properties—specifically NMR chemical shifts in this manuscript—via the open source, high-performance computational chemistry software, NWChem. ISiCLE calculates the NMR chemical shifts of sets of molecules using any available combination of DFT method, solvent, and NMR-active nuclei, using both user-selected reference compounds and/or linear regression methods. Calculated NMR chemical shifts are provided to the user for each molecule, along with comparisons with respect to a number of metrics commonly used in the literature. Here, we demonstrate ISiCLE using a set of 312 molecules, ranging in size up to 90 carbon atoms. For each, calculation of NMR chemical shifts have been performed with 8 different levels of DFT theory, and with solvation effects using the implicit solvent Conductor-like Screening Model. The DFT method dependence of the calculated chemical shifts have been systematically investigated through benchmarking and subsequently compared to experimental data available in the literature. Furthermore, ISiCLE has been applied to a set of 80 methylcyclohexane conformers, combined via Boltzmann weighting and compared to experimental values. We demonstrate that our protocol shows promise in the automation of chemical shift calculations and, ultimately, the expansion of chemical shift libraries.

The origin of the conductivity maximum vs. mixing ratio in pyridine/acetic acid and water/acetic acid

Explanations are provided for the first time for the historically known locations of electrical conductivity maxima versus mixing ratio (mole fraction of acid, x_A) in mixtures of (i) acetic acid with water and (ii) acetic acid with pyridine. To resolve the question for the second system, density-functional-based molecular dynamic simulations were performed, at 1:1, 1:2, 1:3, 1:5, and 1:15 mixing ratios, to gain vital information about speciation. In a zeroth-order picture, the degree of ionization (and hence conductivity) would be maximal at x_A = 0.5, but these two examples see this maximum shifted to the left (water/acetic acid, x_A^max = 0.06), due to improved ion stability when the effective dielectric constant is high (i.e., water-rich mixtures), or right (pyridine/acetic acid x_A^max = 0.83), due to improved acetate stability via "self-solvation" with acetic acid molecules (i.e., acid-rich mixtures) when the dielectric constant is low. A two-parameter equation, with theoretical justification, is shown to reproduce the entire 0 < x_A < 1 range of data for electrical conductivity for both systems. Future work will pursue the applicability of these equations to other amine/carboxylic acid mixtures; preliminary fits to a third system (trimethylamine/acetic acid) give curious parameter values.

Direct evidence of a low barrier hydrogen bond in the catalytic triad of a Serine protease

Serine proteases are one of the largest groups of enzymes, found in both eukaryotes and prokaryotes, and are responsible for many different functions. The detailed information about the hydrogen-bonds in the catalytic triad (Asp…His…Ser) of these enzymes is of importance in order to fully understand the mechanism of action. The aspartate of the triad is hydrogen bonded to the histidine but the exact nature of this bond has been under discussion for some time. It is either a common short ionic hydrogen bond (SIHB) or a delocalized low barrier hydrogen bond (LBHB) were the hydrogen bond is shorter. So far, the evidence for LBHB in proteins have not been conclusive. Here we show clear NMR evidence that LBHB does exist in NS3, a serine protease from Dengue. The one bond coupling constant between the hydrogen and nitrogen was shown to be only 52 Hz instead of the usual 90 Hz. This together with a 1H chemical shift of 19.93 ppm is evidence that the hydrogen bond distance between His and Asp is shorter than for SIHB. Our result clearly shows the existence of LBHB and will help in understanding the mechanism of the catalytic triad in the important group of serine proteases.

Cyclic trimers of phosphinic acids in polar aprotic solvent: symmetry, chirality and H/D isotope effects on NMR chemical shifts

The hydrogen-bonded self-associates of dimethylphosphinic (1), diphenylphosphoric (2), phenylphosphinic (3), and bis(2,4,4-trimethylpentyl)phosphinic (4) acids have been studied by using liquid-state NMR down to 100 K in a low-freezing polar solvent, CDF₃/CDClF₂. The H/D isotope effects on ¹H NMR chemical shifts caused by partial deuteration of hydroxyl groups unambiguously reveal the stoichiometry of the self-associates and the cooperativity of their hydrogen bonds. In all cases, cyclic trimers are the dominant form, while cyclic dimers are present as a minor form for 1 and 2. Due to the asymmetry of substituents, cyclic trimers of 3 exist in two isomeric forms, depending on the orientation of the phenyl groups with respect to the plane of the hydrogen bonds. The racemic mixture of 4 leads to the coexistence of up to 64 isomers of cyclic trimers, many of which are chemically equivalent or effectively isochronous. The mole fractions of such isomers deviate from the statistically expected values. This feature could provide information about the relative stabilization energies of hydrogen-bonded chiral self-associates. The complexation of 4 with SbCl₅ (complex 5) suppresses the self-association and 5 exists exclusively in the monomeric form with chemically non-equivalent ³¹P nuclei in RS, SR and RR/SS forms.

Polar solvent fluctuations drive proton transfer in hydrogen bonded complexes of carboxylic acid with pyridines: NMR, IR and ab initio MD study

We study a series of intermolecular hydrogen-bonded 1 : 1 complexes formed by chloroacetic acid with 19 substituted pyridines and one aliphatic amine dissolved in CD₂Cl₂ at low temperature by ¹H and ¹³C NMR and FTIR spectroscopy. The hydrogen bond geometries in these complexes vary from molecular (O-HN) to zwitterionic (O^-H-N⁺) ones, while NMR spectra show the formation of short strong hydrogen bonds in intermediate cases. Analysis of C[double bond, length as m-dash]O stretching and asymmetric CO₂^- stretching bands in FTIR spectra reveal the presence of proton tautomerism. On the basis of these data, we construct the overall proton transfer pathway. In addition to that, we also study by use of ab initio molecular dynamics the complex formed by chloroacetic acid with 2-methylpyridine, surrounded by 71 CD₂Cl₂ molecules, revealing a dual-maximum distribution of hydrogen bond geometries in solution. The analysis of the calculated trajectory shows that the proton jumps between molecular and zwitterionic forms are indeed driven by dipole-dipole solvent-solute interactions, but the primary cause of the jumps is the formation/breaking of weak CHO bonds from solvent molecules to oxygen atoms of the carboxylate group.

A recognition mechanism study: Luminescent metal-organic framework for the detection of nitro-explosives

This article presents a recognition mechanism for nitro-explosives by the luminescent metal-organic framework 1 (LMOF-1) with the aid of density functional theory (DFT) and time-dependent density functional theory (TDDFT). The behavior of hydrogen bonding between the LMOF-1 and nitro-explosives in the S₁ state is closely associated with the fluorescence properties of the LMOF-1. In our research, we calculated the geometric configuration, ¹H NMR and IR spectra of the Complex 2 formed by LMOF-1 and nitrobenzene in the S₀ and S₁ states. The results showed that the hydrogen bond in the S₁ state was increased, which was unfavorable for the luminescence of LMOF-1. Furthermore, the fluorescence rate of LMOF-1 decreased after encapsulating nitrobenzene into it. These calculated results collectively suggest that LMOF-1 is a potential fluorescence sensor for the detection of nitro-explosives. This research was aiming to provide a better understanding of the recognition mechanism by LMOFs for nitro-explosives.

Ab-Initio Molecular Dynamics Simulations and Calculations of Spectroscopic Parameters in Hydrogen-Bonding Liquids in Confinement (Project 8)

We investigate the effect of several nanoscale confinements on structural and dynamical properties of liquid water and binary aqueous mixtures. By means of molecular dynamics simulations based on density functional theory and atomistic force fields. Our main focus is on the dependence on the structure and the hydrogen-bonding-network of the liquids near the confinement interface at atomistic resolution. As a complementary aspect, spatially resolved profiles of the proton NMR chemical shift values are used to quantify the local strength of the hydrogen-bond-network.

Complexity in Acid-Base Titrations: Multimer Formation Between Phosphoric Acids and Imines

Solutions of Brønsted acids with bases in aprotic solvents are not only common model systems to study the fundamentals of proton transfer pathways but are also highly relevant to Brønsted acid catalysis. Despite their importance the light nature of the proton makes characterization of acid-base aggregates challenging. Here, we track such acid-base interactions over a broad range of relative compositions between diphenyl phosphoric acid and the base quinaldine in dichloromethane, by using a combination of dielectric relaxation and NMR spectroscopy. In contrast to what one would expect for an acid-base titration, we find strong deviations from quantitative proton transfer from the acid to the base. Even for an excess of the base, multimers consisting of one base and at least two acid molecules are formed, in addition to the occurrence of proton transfer from the acid to the base and simultaneous formation of ion pairs. For equimolar mixtures such multimers constitute about one third of all intermolecular aggregates. Quantitative analysis of our results shows that the acid-base association constant is only around six times larger than that for the acid binding to an acid-base dimer, that is, to an already protonated base. Our findings have implications for the interpretation of previous studies of reactive intermediates in organocatalysis and provide a rationale for previously observed nonlinear effects in phosphoric acid catalysis.

Pharmaceutical aspects of salt and cocrystal forms of APIs and characterization challenges

In recent years many efforts have been devoted to the screening and the study of new solid-state forms of old active pharmaceutical ingredients (APIs) with salification or co-crystallization processes, thus modulating final properties without changing the pharmacological nature. Salts, hydrates/solvates, and cocrystals are the common solid-state forms employed. They offer the intriguing possibility of exploring different pharmaceutical properties for a single API in the quest of enhancing the final drug product. New synthetic strategies and advanced characterization techniques have been recently proposed in this hot topic for pharmaceutical companies. This paper reviews the recent progresses in the field particularly focusing on the characterization challenges encountered when the nature of the solid-state form must be determined. The aim of this article is to offer the state-of-the-art on this subject in order to develop new insights and to promote cooperative efforts in the fascinating field of API salt and cocrystal forms.

Intrinsic 37/35Cl and 18/16O isotope shifts in 195Pt and 103Rh NMR of purely inorganic Pt and Rh complexes as unique spectroscopic fingerprints for unambiguous assignment of structure

Well-resolved intrinsic ¹ΔM(^37/35Cl) and ¹ΔM(^18/16O) isotope shifts (where M = ¹⁹⁵Pt or ¹⁰³Rh) are visible in the ¹⁹⁵Pt NMR peak profiles of relatively kinetically inert [PtCl_n(H₂O)_6-n]^4-n (n = 1-6) complexes, their corresponding hydroxido [PtCl_6-n(OH)_n]^2- (n = 1-5/6) anions, and [RhCl_n(H₂O)_6-n]^3-n (n = 3-6) complexes in aqueous solutions at ca. 293 K. Although some such isotope effects have been previously reported, there are very limited published data in the open literature, and the first systematic studies of such intrinsic ¹ΔM(^37/35Cl) and ¹ΔM(^18/16O) isotope effects are reviewed in this perspective. In high magnetic-field NMR spectrometers, the ¹⁹⁵Pt and ¹⁰³Rh NMR peak profiles acquired within a relatively narrow temperature range (288-300 K) constitute unique 'spectroscopic fingerprints', which allow unambiguous structural assignment in solution. Available data for Pt(iv) and Rh(iii) complexes give rise to intrinsic isotope ¹Δδ¹⁹⁵Pt/¹⁰³Rh(^37/35Cl) profiles, which are extraordinarily sensitive to the structure of a particular complex or its geometric isomer. The profiles of aquated Pt(iv) and Rh(iii) complexes in acidic solutions may be resolved at either an isotopologue level only or at both an isotopologue and an isotopomer level depending on the structure. By contrast, in the series of [PtCl_6-n(OH)_n]^2- (n = 1-6) anions, ¹Δδ¹⁹⁵Pt(^37/35Cl) isotope shifts are resolved only at an isotopologue level. Relatively larger ¹Δ¹⁹⁵Pt(^18/16O) isotope shifts obtained by the partial ¹⁸O enrichment of both the [PtCl_n(H₂O)_6-n]^4-n (n = 1-6) and [PtCl_6-n(OH)_n]^2- (n = 1-6) series give rise to remarkable ¹⁹⁵Pt NMR peak profiles showing both ^37/35Cl and ^18/16O shifts. In the [PtCl_6-n(OH)_n]^2- (n = 1-5/6) anions a typical NMR peak profile spanning ∼2 ppm only may be resolved at both the isotopologue and isotopomer levels, depending on whether ^18/16OH^- ions are coordinated trans to chloride ions or not. The potential utility of such ¹Δ¹⁹⁵Pt(^37/35Cl) and ¹Δ¹⁹⁵Pt(^18/16O) isotope shifts in selected practical applications involving such complexes is briefly illustrated.

Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations

The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB) in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.

A novel strategy to construct Janus metallamacrocycles with both a Ru–arene face and an imidazolium face

We report a novel strategy to synthesize Janus metallocyclic Ru–arene complexes with both a Ru–arene face and a didentate imidazolium face, which possess unusual structures and properties.

NMR Spectroscopic Characterization of Charge Assisted Strong Hydrogen Bonds in Brønsted Acid Catalysis

Hydrogen bonding plays a crucial role in Brønsted acid catalysis. However, the hydrogen bond properties responsible for the activation of the substrate are still under debate. Here, we report an in depth study of the properties and geometries of the hydrogen bonds in (R)-TRIP imine complexes (TRIP: 3,3'-Bis(2,4,6-triisopropylphenyl)-1,1'-binaphthyl-2,2'-diylhydrogen phosphate). From NMR spectroscopic investigations 1H and 15N chemical shifts, a Steiner-Limbach correlation, a deuterium isotope effect as well as quantitative values of 1JNH,2hJPH and 3hJPN were used to determine atomic distances (rOH, rNH, rNO) and geometry information. Calculations at SCS-MP2/CBS//TPSS-D3/def2-SVP-level of theory provided potential surfaces, atomic distances and angles. In addition, scalar coupling constants were computed at TPSS-D3/IGLO-III. The combined experimental and theoretical data reveal mainly ion pair complexes providing strong hydrogen bonds with an asymmetric single well potential. The geometries of the hydrogen bonds are not affected by varying the steric or electronic properties of the aromatic imines. Hence, the strong hydrogen bond reduces the degree of freedom of the substrate and acts as a structural anchor in the (R)-TRIP imine complex.

The crucial role of water in shaping low-barrier hydrogen bonds

Low-barrier hydrogen bonds (LBHBs) are key components in a range of chemical processes, often appearing in metal-mediated catalytic applications.

Synthesis of the AB ring system of clifednamide utilizing Claisen rearrangement and Diels–Alder reaction as key steps

A synthesis to the functionalized AB ring system of clifednamide, member of macrocyclic tetramic acid lactams, was developed involving an Ireland–Claisen rearrangement and an intramolecular Diels–Alder reaction.

Influence of hydration on ion-biomolecule interactions: M(+)(indole)(H2O)(n) (M = Na, K; n = 3-6)

The indole functional group can be found in many biologically relevant molecules, such as neurotransmitters, pineal hormones and medicines. Indole has been used as a tractable model to study the hydration structures of biomolecules as well as the interplay of non-covalent interactions within ion-biomolecule-water complexes, which largely determine their structure and dynamics. With three potential binding sites: above the six- or five-member ring, and the N-H group, the competition between π and hydrogen bond interactions involves multiple locations. Electrostatic interactions from monovalent cations are in direct competition with hydrogen bonding interactions, as structural configurations involving both direct cation-indole interactions and cation-water-indole bridging interactions were observed. The different charge densities of Na(+) and K(+) give rise to different structural conformers at the same level of hydration. Infrared spectra with parallel hybrid functional-based calculations and Gibbs free energy calculations revealed rich structural insights into the Na(+)/K(+)(indole)(H2O)3-6 cluster ion complexes. Isotopic (H/D) analyses were applied to decouple the spectral features originating from the OH and NH stretches. Results showed no evidence of direct interaction between water and the NH group of indole (via a σ-hydrogen bond) at current levels of hydration with the incorporation of cations. Hydrogen bonding to a π-system, however, was ubiquitous at hydration levels between two and five.

A sensor for formaldehyde detection: luminescent metal–organic framework [Zn2(H2L)(2,2′-bpy)2(H2O)]n

The comparison between the two systems shows that the encapsulation of formaldehyde can affect the luminescence behavior of [Zn₂(H₂L)(2,2′-bpy)₂(H₂O)]_n.

Association and liquid structure of pyridine–acetic acid mixtures determined from neutron scattering using a ‘free proton’ EPSR simulation model

Hydrogen-bonded molecular acetic acid chains are observed in acid–base mixtures from small angle neutron diffraction.

The C113D mutation in human Pin1 causes allosteric structural changes in the phosphate binding pocket of the PPIase domain through the tug of war in the dual-histidine motif

Pin1 peptidyl-prolyl isomerase (PPIase) catalyzes specifically the pSer/pThr-Pro motif. The cis-trans isomerization mechanism has been studied by various approaches, including X-ray crystallography, site-directed mutagenesis, and the kinetic isotope effect on isomerization. However, a complete picture of the reaction mechanism remains elusive. On the basis of the X-ray structure of Pin1, residue C113 was proposed to play a nucleophile attacker to catalyze the isomerization. The controversial result that the C113D Pin1 mutant retains the activity, albeit at a reduced level, challenges the importance of C113 as a catalyst. To facilitate our understanding of the Pin1 isomerization process, we compared the structures and dynamics of the wild type with those of the C113D mutant Pin1 PPIase domains (residues 51-163). We found the C113D mutation disturbed the hydrogen bonds between the conserved histidine residues, H59 and H157 ("dual-histidine motif"); H59 imidazole forms a stable hydrogen bond to H157 in the wild type, whereas it has a strong hydrogen bond to D113 with weakened bonding to H157 in the C113D mutant. The C113D mutation unbalanced the hydrogen bonding tug of war for H59 between C113/D113 and H157 and destabilized the catalytic site structure, which eventually resulted in an altered conformation of the basic triad (K63, R68, and R69) that binds to the phosphate group in a substrate. The change in the basic triad structure could explain the severely weakened substrate binding ability of the C113D mutant. Overall, this work demonstrated that C113 plays a role in keeping the catalytic site in an active fold, which has never before been described.

Hydrogen bond coupling in sodium dihydrogen triacetate

The coupling of hydrogen bonds is central to structures and functions of biological systems. Hydrogen bond coupling in sodium dihydrogen triacetate (SDHTA) is investigated as a model for the hydrogen bonded systems of the type O-H…O. The two-dimensional potential energy surface is derived from the full-dimensional one by selecting the relevant vibrational modes of the hydrogen bonds. The potential energy surfaces in terms of normal modes describing the anharmonic motion in the vicinity of the equilibrium geometry of SDHTA are calculated for the different species, namely, HH, HD, DH, and DD isotopomers. The ground state wave functions and their relation to the hydrogen bond structural parameters are discussed. It has been found that the hydrogen bonds in SDHTA are uncoupled, that is elongation of the deuterated hydrogen bond does not affect the non-deuterated one.

Measurement of proton tunneling in short hydrogen bonds in single crystals of 3,5 pyridinedicarboxylic acid using nuclear magnetic resonance spectroscopy

In this Letter, we present NMR spin-lattice and relaxometry data for proton transfer in one of the shortest known N-H⋯O hydrogen bonds in a single crystal of 3,5 pyridinedicarboxylic acid (35PDCA). It is widely believed that proton transfer by quantum tunneling does not occur in short hydrogen bonds since the ground state energy level lies above the potential barrier, yet these data show a temperature independent, proton tunneling rate below 77 K and a clear deviation from classical dynamics below 91 K. This study therefore suggests that proton tunneling occurs in all hydrogen bonds at low temperature and the crossover temperature to classical hopping must be determined when evaluating whether proton tunneling persists at higher temperature, for example in enzyme catalysis under physiological conditions.

NMR study of short β(1-3)-glucans provides insights into the structure and interaction with Dectin-1

β(1-3)-Glucans, abundant in fungi, have the potential to activate the innate immune response against various pathogens. Although part of the action is exerted through the C-type lectin-like receptor Dectin-1, details of the interaction mechanism with respect to glucan chain-length remain unclear. In this study, we investigated a set of short β(1-3)-glucans with varying degree of polymerization (DP); 3, 6, 7, 16, and laminarin (average DP; 25), analyzing the relationship between the structure and interaction with the C-type lectin-like domain (CTLD) of Dectin-1. The interaction of short β(1-3)-glucans (DP6, DP16, and laminarin) with the CTLD of Dectin-1 was systematically analyzed by (1)H-NMR titration as well as by saturation transfer difference (STD)-NMR. The domain interacted weakly with DP6, moderately with DP16 and strongly with laminarin, the latter plausibly forming oligomeric protein-laminarin complexes. To obtain structural insights of short β(1-3)-glucans, the exchange rates of hydroxy protons were analyzed by deuterium induced (13)C-NMR isotope shifts. The hydroxy proton at C4 of laminarin has slower exchange with the solvent than those of DP7 and DP16, suggesting that laminarin has a secondary structure. Diffusion ordered spectroscopy revealed that none of the short β(1-3)-glucans including laminarin forms a double or triple helix in water. Insights into the interaction of the short β(1-3)-glucans with Dectin-1 CTLD provide a basis to understand the molecular mechanisms of β-glucan recognition and cellular activation by Dectin-1.

NMR and FT-IR Studies on the Association of Derivatives of Thymidine, Adenosine, and 6-N-Methyl-Adenosine in Aprotic Solvents

Associates of 3',5'-O-TBDMS protected derivatives of the 2'-deoxy forms of the nucleosides adenosine, 6-N-methyl-adenosine and thymidine (henceforward simply addressed by their parents' names) and further model systems in dichloromethane and Freon (CDClF2/CDF3) solutions are studied at low temperatures by 1H NMR and FT-IR spectroscopy. N⋯N distances in hydrogen bonds are estimated from chemical shifts of protons in hydrogen bonds employing geometric and spectroscopic hydrogen bond correlations. These distances are in turn employed to derive N–H stretching frequencies from IR spectroscopic hydrogen bond correlations which may be compared to corresponding experimental results. Three isomeric hydrogen bonded dimers of thymidine are characterized in Freon solution at 120 K. Binary associates of thymidine and a series of pyridines are studied; estimated N⋯N distances in the range of 3.08 to 2.85 Å are qualitatively correlated to shifts of N–H stretching bands where in all cases considerable contributions are found in the spectral region below 3000 cm-1. For adenosine, three isomeric binary associates with 4-nitrophenol are found allowing for an assessment of site-specific acceptor capabilities. In associates of thymidine and adenosine, Watson-Crick and Hoogsteen type 1:1 associates (estimated N⋯N distances of 2.85 and 2.90 Å) as well as 2:1 associates bearing only marginally longer H-bonds could be characterized. Two 1:1 associates between thymidine and 6-N-methyl-adenosine are described that are exclusively bonded via N–H⋯N bridges of about 2.97 and 3.08 Å for Watson-Crick and Hoogsteen sites, respectively, which leads to the conclusion that cooperative effects among coupled N–H⋯O and N–H⋯N hydrogen bonds in A-T base pairs are significant as formation of the N–H⋯O bond induces a contraction of around 0.15 Å in the neighboring N–H⋯N bond.