Engagement of CF3 Group in N–H···F–C Hydrogen Bond in the Solution State: NMR Spectroscopy and MD Simulation Studies

Illuminating the multiple Lewis acidity of triaryl-boranes via atropisomeric dative adducts

Using the principle that constrained conformational spaces can generate novel and hidden molecular properties, we challenged the commonly held perception that a single-centered Lewis acid reacting with a single-centered Lewis base always forms a single Lewis adduct. Accordingly, the emergence of single-centered but multiple Lewis acidity among sterically hindered and non-symmetric triaryl-boranes is reported. These Lewis acids feature several diastereotopic faces providing multiple binding sites at the same Lewis acid center in the interaction with Lewis bases giving rise to adducts with diastereomeric structures. We demonstrate that with a proper choice of the base, atropisomeric adduct species can be formed that interconvert via the dissociative mechanism rather than conformational isomerism. The existence of this exotic and peculiar molecular phenomenon was experimentally confirmed by the formation of atropisomeric piperidine-borane adducts using state-of-the-art NMR techniques in combination with computational methods.

Can the -CF3 Group Act as a Tight, Well-Defined Hydrogen Bond Acceptor? A Clear Crystallographic CF2-F···H-N+ Interaction Says Yes

The CF3 group is well noted for being noninteractive with other functional groups. In this Note, we present a highly rigid model system containing a significant hydrogen bonding interaction between a charged N-H donor and a CF3 acceptor that challenges this accepted wisdom. Spectroscopic and single crystal X-ray crystallography data characterize this interaction, consistent with a weak to moderate hydrogen bond that would be difficult to observe in an intermolecular system.

β-Cyclodextrin Supramolecular Recognition of bis-Cationic Dithienylethenes

The supramolecular interactions in water between β-cyclodextrin and the open and closed photochromic forms of two bis-cationic dithienylethenes, characterized by different electronic properties, were investigated aiming at underlying the key aspects of the recognition process. The dithienylethene equipped with the cyclopentenyl unit showed a difference in binding free energies to the β-cyclodextrin between the open and closed photochromic forms of about 1 kJ/mol. Conversely, the dithienylethene equipped with the perfluorinated cyclopentenyl unit not only was a better guest but showed a three times higher difference in the binding of free energies between the open and closed isomers.

2-Trifluoromethyl-6-mercurianiline Nucleotide, a Sensitive 19F NMR Probe for Hg(II)-mediated Base Pairing

A 2-trifluoromethylaniline C-nucleoside was synthesized, incorporated in the middle of an oligonucleotide, and mercurated. The affinity of the mercurated oligonucleotide toward complementary strands placing each of the canonical nucleobases opposite to the organomercury nucleobase analogue was examined by ultraviolet (UV), circular dichroism (CD), and 19F NMR spectroscopy analyses. According to the UV melting profile analysis, the organomercury nucleobase analogue showed increased affinities in the order T > G > C > A. The CD profiles indicated the typical B-type helix in each case. The 19F resonance signal proved sensitive for the local environmental changes, showing clearly distinct signals for the duplexes with different opposing nucleobases. Furthermore, valuable information on the mercurated oligonucleotide and its binding to complementary strands at varying temperature could be obtained by 19F NMR spectroscopy.

Exploration of 7-azaindole-coumaranone hybrids and their analogues as protein kinase inhibitors

7-Azaindole has been labelled a privileged scaffold for the design of new potent inhibitors of protein kinases. In this paper, we determined the inhibition profiles of novel mono- and disubstituted derivatives of 7-azaindole-coumaranone hybrids on various disease-related protein kinases. Eight hit compounds were identified, including a potent Haspin inhibitor with an IC₅₀ value of 0.15 μM. An interesting observation was that all active monosubstituted compounds displayed dual inhibition for Haspin and GSK-3β, while disubstituted derivatives inhibited GSK-3β and LmCK1 from Leishmania major parasite. Analyses of structure activity relationships (SARs) also revealed that mono-substitution with para-fluorobenzyloxy ring produced an equipotent inhibition of Haspin and GSK-3β. Haspin and GSK-3β are relevant targets for developing new anticancer agents while LmCK1 is an innovative target for leishmanicidal drugs. Novel compounds reported in this paper constitute promising starting points for the development of new anticancer and leishmanicidal drugs.

Competing HB acceptors: an extensive NMR investigations corroborated by single crystal XRD and DFT calculations

A series of N-benzoylanthranilamide derivatives have been synthesized with the substitution of competitive HB acceptors and investigated by NMR spectroscopy and single crystal XRD. The interesting rivalry for HB acceptance between [double bond splayed left]C[double bond, length as m-dash]O and X (F or OMe) is observed in the investigated molecules which leads to an unusual increase in the electron density at the site of one of the NH protons, reflecting in the high field resonance in the 1H NMR spectrum. The NMR experimental findings and single crystal XRD are further reinforced by the DFT studies.

Studies of novel trifluoroacetylated diaryl hydrazone molecular photoswitches in solution and in the solid state

Photoisomerization of trifluoroacetylated diaryl hydrazones induces a change in color due to the formation of a new hydrogen bond in solution and in the solid state.

The shuttling mechanism of foldaxanes: more than just translocation and rotation

Tailoring the structures of nanomachines to achieve specific functions is one of the major challenges in chemistry. Disentangling the different movements of nanomachines is critical to characterize their functions. Here, the motions within one kind of molecular machine, a foldaxane, composed of a foldamer with a spring-like conformation on an axle have been examined at the molecular level. With the aid of molecular dynamics simulations and enhanced sampling methods, the free-energy landscape characterizing the shuttling of the foldaxane has been drawn. The calculated free-energy barrier, amounting to 20.7 kcal mol^-1, is in good agreement with experiments. Further analysis reveals that the predominant contribution to the free-energy barrier stems from the disruption of the hydrogen bonds between the foldamer and the thread. In the absence of hydrogen bonding interactions between the terminals of the foldamer and the thread, shrinkage and swelling movements of the foldamer have been identified and investigated in detail. By deciphering the intricate mechanism of how the foldaxane shuttles, our understanding of motions within molecular machines is expected to be improved, which will, in turn, assist the construction of molecular machines with specific functions.

Building blocks for the chemistry of perfluorinated alkoxyaluminates [Al{OC(CF3)3}4]-: simplified preparation and characterization of Li+-Cs+, Ag+, NH4+, N2H5+ and N2H7+ salts

Advanced weakly coordinating anions (WCAs) significantly facilitate synthesis of various exotic chemical compounds and novel, potentially useful materials. One of such anions - [Al{OC(CF₃)₃}₄]^-, denoted [Al(OR^F)₄]^-, appears particularly convenient, as it can be easily prepared from the commercially available alanates and HOC(CF₃)₃. Here we present a thorough characterization of a series of solvent-free M[Al(OR^F)₄] salts, M = Li-Cs, Ag, NH₄, N₂H₅ and N₂H₇, and related compounds of monovalent cations, which are crucial starting materials for further work with these species. Notably, the corresponding synthetic protocols are updated by an improved method for fast, facile and easily scalable synthesis of Li[Al(OR^F)₄], which remains the most useful primary source of the anion. The physico-chemical properties of these salts including crystal structures, thermal stability by TG/DSC, vibrational spectra as well as solubility are discussed in a systematic fashion.

The Role of Fluorinated IL as an Interfacial Agent in P(VDF-CTFE)/Graphene Composite Films

The incorporation of graphene into a polymer matrix can endow composites with extended functions. However, it is difficult to well disperse pristine graphene into a polymer matrix in order to obtain polymer nanocomposites due to the lack of functional groups on the surface for bonding with a polymer matrix. Herein, we investigated the role of fluorinated ionic liquid (IL) as a new interfacial agent in poly(vinylidene fluoride-co-chlorotrifluoroethylene) (P(VDF-CTFE))/graphene composite films. First, a task-specific IL, perfluorooctyltriphenylphosphonium iodide (IL-C8F13), was synthesized and adsorbed on the surface of graphene oxide (GO) and reduced graphene oxide (rGO) for making functional nanofillers which were capable of being incorporated into the P(VDF-CTFE) matrix. The cation structure of IL combined three phenyls (potential π–π interactions with graphene) and a short fluorinated chain (enhanced miscibility with fluorinated matrix via dipolar interactions) to make a compatible graphene filler and P(VDF-CTFE) matrix at the interface among them. Second, two series of P(VDF-CTFE)/GO-IL and P(VDF-CTFE)/rGO-IL composites with different loading contents were prepared with the goal of providing an understanding of the mechanism of interfacial interactions. This paper investigated the difference in the interaction model between GO with IL and rGO with IL. Subsequently, the interfacial effect of IL on the properties of P(VDF-CTFE)/graphene composites, such as crystallization, chain segmental relaxation behavior, dispersion, and the final dielectric properties will be further studied.

DDX3X Helicase Inhibitors as a New Strategy To Fight the West Nile Virus Infection

Increased frequency of arbovirus outbreaks in the last 10 years represents an important emergence for global health. Climate warming, extensive urbanization of tropical regions, and human migration flows facilitate the expansion of anthropophilic mosquitos and the emerging or re-emerging of new viral infections. Only recently the human adenosinetriphosphatase/RNA helicase X-linked DEAD-box polypeptide 3 (DDX3X) emerged as a novel therapeutic target in the fight against infectious diseases. Herein, starting from our previous studies, a new family of DDX3X inhibitors was designed, synthesized, validated on the target enzyme, and evaluated against the West Nile virus (WNV) infection. Time of addition experiments after virus infection indicated that the compounds exerted their antiviral activities after the entry process, likely at the protein translation step of WNV replication. Finally, the most interesting compounds were then analyzed for their in vitro pharmacokinetic parameters, revealing favorable absorption, distribution, metabolism, and excretion values. The good safety profile together with a good activity against WNV for which no treatments are currently available, make this new class of molecules a good starting point for further in vivo studies.

Quadruply N-methylated octaphyrin: a helical macrocycle exhibiting chiroptical properties and dynamic conformation changes correlated with helical and inner N-methyl orientations

[38]Octaphyrin(1.1.1.1.1.1.1.1) bearing four methyl moieties at the inner nitrogen sites has been synthesized. This expanded porphyrin has helical chirality as correlated with the orientations of the inner N-methyl groups, exhibiting chiroptical properties as observed in CD Cotton effects from the enantiomers through optical resolution. The chirality of the octaphyrin was retained at r.t. but the racemization occurred at higher temperature as examined by CD spectral changes. The dynamic conversion processes between the enantiomers were investigated by theoretical studies, suggesting the plausible pathways via the intermediates with appropriate conformations.

Retention of strong intramolecular hydrogen bonds in high polarity solvents in binaphthalene–benzamide derivatives: extensive NMR studies

Advanced multidimensional NMR techniques have been employed to investigate the intramolecular hydrogen bonds (HBs) in a series of N,N′-([1,1′-binaphthalene]-2,2′-diyl)bis(benzamide) derivatives, with the site-specific substitution of different functional groups. The existence of intramolecular HBs and the elimination of any molecular aggregation and possible intermolecular HBs are ascertained by various experimental NMR techniques, including solvent polarity dependent modifications of HB strengths. In the fluorine substituted derivative, direct evidence for the engagement of organic fluorine in HB is obtained by the detection of heteronuclear through-space correlation and the coupling between two NMR active nuclei where the transmission of spin polarization is mediated through HBs (^1hJ_FH). The extent of reduction in the strength of ^1hJ_FH on dilution with high polarity solvents directly provided the qualitative measure of HB strength. The HB, although becoming weakened, does not get nullified even in pure high polarity solvent, which is attributed to the structural constraints. The rate of exchange of a labile hydrogen atom with the deuterium of the solvent permitted the measurement of their half-lives, that are correlated to the relative strengths of HBs. The experimental NMR findings are further validated by XRD and DFT-based theoretical computations, such as, NCI and QTAIM.

NMR studies reveal very strong hydrogen bond unbreakable even in high polarity solvents.

Fluorine-Substituted Pyrrolo[2,3- d]Pyrimidine Analogues with Tumor Targeting via Cellular Uptake by Folate Receptor α and the Proton-Coupled Folate Transporter and Inhibition of de Novo Purine Nucleotide Biosynthesis

Novel fluorinated 2-amino-4-oxo-6-substituted pyrrolo[2,3- d]pyrimidine analogues 7-12 were synthesized and tested for selective cellular uptake by folate receptors (FRs) α and β or the proton-coupled folate transporter (PCFT) and for antitumor efficacy. Compounds 8, 9, 11, and 12 showed increased in vitro antiproliferative activities (∼11-fold) over the nonfluorinated analogues 2, 3, 5, and 6 toward engineered Chinese hamster ovary and HeLa cells expressing FRs or PCFT. Compounds 8, 9, 11, and 12 also inhibited proliferation of IGROV1 and A2780 epithelial ovarian cancer cells; in IGROV1 cells with knockdown of FRα, 9, 11, and 12 showed sustained inhibition associated with uptake by PCFT. All compounds inhibited glycinamide ribonucleotide formyltransferase, a key enzyme in the de novo purine biosynthesis pathway. Molecular modeling studies validated in vitro cell-based results. NMR evidence supports the presence of an intramolecular fluorine-hydrogen bond. Potent in vivo efficacy of 11 was established with IGROV1 xenografts in severe compromised immunodeficient mice.

Structure-Based Analysis of Boronic Acids as Inhibitors of Acinetobacter-Derived Cephalosporinase-7, a Unique Class C β-Lactamase

Acinetobacter baumannii is a multidrug resistant pathogen that infects more than 12 000 patients each year in the US. Much of the resistance to β-lactam antibiotics in Acinetobacter spp. is mediated by class C β-lactamases known as Acinetobacter-derived cephalosporinases (ADCs). ADCs are unaffected by clinically used β-lactam-based β-lactamase inhibitors. In this study, five boronic acid transition state analog inhibitors (BATSIs) were evaluated for inhibition of the class C cephalosporinase ADC-7. Our goal was to explore the properties of BATSIs designed to probe the R1 binding site. K_i values ranged from low micromolar to subnanomolar, and circular dichroism (CD) demonstrated that each inhibitor stabilizes the β-lactamase-inhibitor complexes. Additionally, X-ray crystal structures of ADC-7 in complex with five inhibitors were determined (resolutions from 1.80 to 2.09 Å). In the ADC-7/CR192 complex, the BATSI with the lowest K_i (0.45 nM) and greatest Δ T_m (+9 °C), a trifluoromethyl substituent, interacts with Arg340. Arg340 is unique to ADCs and may play an important role in the inhibition of ADC-7. The ADC-7/BATSI complexes determined in this study shed light into the unique recognition sites in ADC enzymes and also offer insight into further structure-based optimization of these inhibitors.

Intramolecular Hydrogen Bonding Appetency for Conformational Penchants in Oxalohydrazide Fluoro Derivatives: NMR, MD, QTAIM, and NCI Studies

The conformational stability of synthesized diphenyloxalohydrazide and dibenzoyloxalohydrazide fluoro derivatives has been investigated by extensive NMR studies that are ascertained by various levels of theoretical calculations. Two-dimensional ¹H-¹⁹F HOESY NMR experiments revealed the close spatial proximity between two NMR-active nuclei, confirming the hydrogen bond (HB)-mediated interaction between them, further aiding in establishing the probable stable conformations of these molecules. The relaxed potential energy scan disclosed the energy-minimized most stable structure among the several possible multiple conformations, which is in concurrence with NMR interpretations. Atomistic molecular dynamics simulations have been employed to unequivocally establish the conformational stability and the nature of HB formation at varied temperatures. With the possibility of occurrence of a number of probable conformations, the percentage of occurrences of different types of HBs in them was determined by MD simulations. Their population analysis was carried out using a Boltzmann distribution, in addition to deriving their Gibbs free energies. The molecular interactions governing the stable conformations have not only been ascertained by experimental NMR interpretations but also corroborated by other theoretical computations, viz., quantum theory of atoms in molecules (QTAIM) and noncovalent interaction (NCI).

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.

Molecular interactions between DOPA and surfaces with different functional groups: a chemical force microscopy study

The adhesion of mussel foot proteins (Mfps) to a variety of surfaces has been widely investigated, but the mechanisms behind the mussel adhesion to surfaces with different properties are far from being understood.

Catalytic enantioselective addition of organoboron reagents to fluoroketones controlled by electrostatic interactions

Organofluorine compounds are central to modern chemistry, and broadly applicable transformations that generate them efficiently and enantioselectively are in much demand. Here we introduce efficient catalytic methods for the addition of allyl and allenyl organoboron reagents to fluorine-substituted ketones. These reactions are facilitated by readily and inexpensively available catalysts and deliver versatile and otherwise difficult-to-access tertiary homoallylic alcohols in up to 98% yield and >99:1 enantiomeric ratio. Utility is highlighted by a concise enantioselective approach to the synthesis of the antiparasitic drug fluralaner (Bravecto, presently sold as the racemate). Different forms of ammonium-organofluorine interactions play a key role in the control of enantioselectivity. The greater understanding of various non-bonding interactions afforded by these studies should facilitate the future development of transformations that involve fluoroorganic entities.

Intramolecular hydrogen bonds involving organic fluorine in the derivatives of hydrazides: an NMR investigation substantiated by DFT based theoretical calculations

The rare examples of intramolecular hydrogen bonds (HB) of the type the N-H∙∙∙F-C, detected in a low polarity solvent in the derivatives of hydrazides, by utilizing one and two-dimensional solution state multinuclear NMR techniques, are reported. The observation of through-space couplings, such as, (1h)JFH, and (1h)JFN, provides direct evidence for the existence of intra-molecular HB. Solvent induced perturbations and the variable temperature NMR experiments unambiguously establish the presence of intramolecular HB. The existence of multiple conformers in some of the investigated molecules is also revealed by two dimensional HOESY and (15)N-(1)H HSQC experiments. The (1)H DOSY experimental results discard any possibility of self or cross dimerization of the molecules. The derived NMR experimental results are further substantiated by Density Function Theory (DFT) based Non Covalent Interaction (NCI), and Quantum Theory of Atom in Molecule (QTAIM) calculations. The NCI calculations served as a very sensitive tool for detection of non-covalent interactions and also confirm the presence of bifurcated HBs.

The strengths and weaknesses of NMR spectroscopy and mass spectrometry with particular focus on metabolomics research

Mass spectrometry (MS) and nuclear magnetic resonance (NMR) have evolved as the most common techniques in metabolomics studies, and each brings its own advantages and limitations. Unlike MS spectrometry, NMR spectroscopy is quantitative and does not require extra steps for sample preparation, such as separation or derivatization. Although the sensitivity of NMR spectroscopy has increased enormously and improvements continue to emerge steadily, this remains a weak point for NMR compared with MS. MS-based metabolomics provides an excellent approach that can offer a combined sensitivity and selectivity platform for metabolomics research. Moreover, different MS approaches such as different ionization techniques and mass analyzer technology can be used in order to increase the number of metabolites that can be detected. In this chapter, the advantages, limitations, strengths, and weaknesses of NMR and MS as tools applicable to metabolomics research are highlighted.

Organic fluorine involved intramolecular hydrogen bonds in the derivatives of imides: NMR evidence corroborated by DFT based theoretical calculations

The rare occurrence of intramolecular hydrogen bonds (HBs) of the type N–H⋯F–C is detected in the derivatives of imides in a low polarity solvent by using multi-dimensional and multinuclear NMR experiments.

Three centered hydrogen bonds of the type CO⋯H(N)⋯X–C in diphenyloxamide derivatives involving halogens and a rotating CF3 group: NMR, QTAIM, NCI and NBO studies

The existence of three centered CO⋯H(N)⋯X–C hydrogen bonds (H-bonds) involving organic fluorine and other halogens in diphenyloxamide derivatives has been explored by NMR spectroscopy and quantum theoretical studies.

RB69 DNA polymerase structure, kinetics, and fidelity

This review will summarize our structural and kinetic studies of RB69 DNA polymerase (RB69pol) as well as selected variants of the wild-type enzyme that were undertaken to obtain a deeper understanding of the exquisitely high fidelity of B family replicative DNA polymerases. We discuss how the structures of the various RB69pol ternary complexes can be used to rationalize the results obtained from pre-steady-state kinetic assays. Our main findings can be summarized as follows. (i) Interbase hydrogen bond interactions can increase catalytic efficiency by 5000-fold; meanwhile, base selectivity is not solely determined by the number of hydrogen bonds between the incoming dNTP and the templating base. (ii) Minor-groove hydrogen bond interactions at positions n – 1 and n – 2 of the primer strand and position n – 1 of the template strand in RB69pol ternary complexes are essential for efficient primer extension and base selectivity. (iii) Partial charge interactions among the incoming dNTP, the penultimate base pair, and the hydration shell surrounding the incoming dNTP modulate nucleotide insertion efficiency and base selectivity. (iv) Steric clashes between mismatched incoming dNTPs and templating bases with amino acid side chains in the nascent base pair binding pocket (NBP) as well as weak interactions and large gaps between the incoming dNTPs and the templating base are some of the reasons that incorrect dNTPs are incorporated so inefficiently by wild-type RB69pol. In addition, we developed a tC°–tC_nitro Förster resonance energy transfer assay to monitor partitioning of the primer terminus between the polymerase and exonuclease subdomains.

Pure shift NMR approach for fast and accurate extraction of heteronuclear couplings

An NMR experiment for the direct determination of heteronuclear couplings from the severely overlapped ¹H NMR spectrum.