Microwave and Quantum Chemical Study of Intramolecular Hydrogen Bonding in 2-Propynylhydrazine (HC≡CCH2NHNH2)

The microwave spectrum of 2-propynylhydrazine (HC≡CCH2NHNH2) was investigated in the 23-124 GHz spectral interval. The spectra of two conformers denoted I and II were assigned. I is the lower-energy form, and relative intensity measurements yielded an internal energy difference of 3.0(4) kJ/mol between I and II. The spectra of the ground and five vibrationally excited states were assigned for I, whereas only the spectrum of the ground vibrational state was assigned for II. Both I and II are each stabilized simultaneously by two intramolecular hydrogen bonds. The first of these hydrogen bonds is formed between the hydrogen atom of the -NH- part of the hydrazino group, and the second internal hydrogen bond is formed between one of the hydrogen atoms of the -NH2 part. The π-electrons of the triple bond is thus shared by these two hydrogen atoms. The shortest contact between a hydrogen atom of the hydrazino group and the π-electrons of the ethynyl group is found in lower-energy conformer I. The conformational properties of 2-propynylhydrazine were explored by MP2/cc-pVTZ and CCSD/cc-pVQZ calculations. The CCSD method predicts that seven rotameric forms exist for this compound. Five of these rotamers are stabilized by internal hydrogen bonding. The simultaneous sharing of the π-electrons of the triple bond by two hydrogen atoms occurs only in Conformers I and II, which are predicted to be the two forms with the lowest energies, with I 2.52 kJ/mol lower in energy than II. The effective rotational constants of the ground vibrational states of I and II were predicted by a combination of MP2 and CCSD calculations, whereas centrifugal distortion constants and vibration-rotation constants were calculated by the MP2 method. The theoretical spectroscopic constants are compared with the experimental counterparts. It is concluded that more refined calculations are necessary to obtain complete agreement.

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.

On the origin of donor O-H bond weakening in phenol-water complexes

Matrix isolation infrared spectroscopy has been used to investigate intermolecular interactions in a series of binary O-H⋯O hydrogen bonded phenol-water complexes where water is the common acceptor. The interaction at the binding site has been tuned by incorporating multiple fluorine substitutions at different aromatic ring sites of the phenol moiety. The spectral effects for the aforesaid chemical changes are manifested in the infrared spectra of the complexes as systematic increase in spectral shift of the phenolic O-H stretching fundamental (ΔνO-H). While νO-H bands of the monomers of all the fluorophenols appear within a very narrow frequency range, the increase in ΔνO-H of the complexes from phenol to pentafluorophenol is very large, nearly 90%. The observed values of ΔνO-H do not show a linear correlation with the total binding energies (ΔEb) of the complexes, expected according to Badger-Bauer rule. However, in the same ΔνO-H vs ΔEb plot, nice linear correlations are revealed if the complexes of ortho-fluorophenols are treated separately from their meta/para-substituted analogues. The observations imply that in spite of having the same binding site (O-H⋯O) and the same chemical identities (phenolic), the complexes of ortho and non-ortho fluorophenols do not belong, from the viewpoint of detailed molecular interactions, to a homologous series. Linear correlations of ΔνO-H are, however, observed with respect to the electrostatic component of ΔEb as well as the quantum mechanical charge transfer interaction energy (ECT). From quantitative viewpoint, the latter correlation along with the associated electronic structure parameters appears more satisfactory. It has also been noted that the observed ΔνO-H values of the complexes display a linear relationship with the aqueous phase pKa values of the respective phenol derivatives.

Design and Evaluation of a Novel Felbinac Transdermal Patch: Combining Ion-Pair and Chemical Enhancer Strategy

The aim of this study was to design a novel felbinac (FEL) patch with significantly higher (P < 0.05) skin permeation amount than the commercial product SELTOUCH® using ion-pair and chemical enhancer strategy, overcoming the disadvantage of the large application area of SELTOUCH®. Six complexes of FEL with organic amines diethylamine (DEA), triethylamine (TEA), N-(2'-hydroxy-ethanol)-piperdine (HEPP), monoethanolamine (MEtA), diethanolamine (DEtA), and triethanolamine (TEtA) were prepared by ion-pair interaction, and their formation were confirmed by differential scanning calorimetry (DSC), powder X-ray diffraction (pXRD), infared spectroscopy (IR), and proton nuclear magnetic resonance spectroscopy ((1)H-NMR). Subsequently, the effect of ion-pair complexes and chemical enhancers were investigated through in vitro and in vivo experiments using rabbit abdominal skin. Results showed that FEL-TEA was the most potential candidate both in isopropyl palmitate (IPP) solution and transdermal patches. Combining use of 10% N-dodecylazepan-2-one (Azone), the optimized FEL-TEA patch achieved a flux of 18.29 ± 2.59 μg/cm(2)/h, which was twice the amount of the product SELTOUCH® (J = 9.18 ± 1.26 μg/cm(2)/h). Similarly, the area under the concentration curve from time 0 to time t (AUC0-t ) in FEL-TEA patch group (15.94 ± 3.58 h.μg/mL) was also twice as that in SELTOUCH® group (7.31 ± 1.16 h.μg/mL). Furthermore, the in vitro skin permeation results of FEL-TEA patch was found to have a good correlation with the in vivo absorption results in rabbit. These findings indicated that a combination of ion-pair and chemical enhancer strategy could be useful in developing a novel transdermal patch of FEL.

Hydrogen Bonds Computing Server (HBCS): an online web server to compute hydrogen-bond interactions and their precision

Hydrogen bonds in biological macromolecules play significant structural and functional roles. They are the key contributors to most of the interactions without which no living system exists. In view of this, a web-based computing server, the Hydrogen Bonds Computing Server (HBCS), has been developed to compute hydrogen-bond interactions and their standard deviations for any given macromolecular structure. The computing server is connected to a locally maintained Protein Data Bank (PDB) archive. Thus, the user can calculate the above parameters for any deposited structure, and options have also been provided for the user to upload a structure in PDB format from the client machine. In addition, the server has been interfaced with the molecular viewers Jmol and JSmol to visualize the hydrogen-bond interactions. The proposed server is freely available and accessible via the World Wide Web at http://bioserver1.physics.iisc.ernet.in/hbcs/.

Reliable vibrational wavenumbers for C=O and N-H stretchings of isolated and hydrogen-bonded nucleic acid bases

The accurate prediction of vibrational wavenumbers for functional groups involved in hydrogen-bonded bridges remains an important challenge for computational spectroscopy. For the specific case of the C=O and N-H stretching modes of nucleobases and their oligomers, the paucity of experimental reference values needs to be compensated by reliable computational data, which require the use of approaches going beyond the standard harmonic oscillator model. Test computations performed for model systems (formamide, acetamide and their cyclic homodimers) in the framework of the second order vibrational perturbation theory (VPT2) confirmed that anharmonic corrections can be safely computed by global hybrid (GHF) or double hybrid (DHF) functionals, whereas the harmonic part is particularly challenging. As a matter of fact, GHFs perform quite poorly and even DHFs, while fully satisfactory for C=O stretchings, face unexpected difficulties when dealing with N-H stretchings. On these grounds, a linear regression for N-H stretchings has been obtained and validated for the heterodimers formed by 4-aminopyrimidine with 6-methyl-4-pyrimidinone (4APM-M4PMN) and by uracil with water. In view of the good performance of this computational model, we have built a training set of B2PLYP-D3/maug-cc-pVTZ harmonic wavenumbers (including linear regression scaling for N-H) for six-different uracil dimers and a validation set including 4APM-M4PMN, one of the most stable hydrogen-bonded adenine homodimers, as well as the adenine-uracil, adenine-thymine, guanine-cytosine and adenine-4-thiouracil heterodimers. Because of the unfavourable scaling of DHF harmonic wavenumbers with the dimensions of the investigated systems, we have optimized a linear regression of B3LYP-D3/N07D harmonic wavenumbers for the training set, which has been next checked against the validation set. This relatively cheap model, which shows very good agreement with experimental data (average errors of about 10 cm(-1)), paves the route toward a reliable analysis of spectroscopic signatures for larger polynucleotides.

On the satisfaction of backbone-carbonyl lone pairs of electrons in protein structures

Protein structures are stabilized by a variety of noncovalent interactions (NCIs), including the hydrophobic effect, hydrogen bonds, electrostatic forces and van der Waals’ interactions. Our knowledge of the contributions of NCIs, and the interplay between them remains incomplete. This has implications for computational modeling of NCIs, and our ability to understand and predict protein structure, stability, and function. One consideration is the satisfaction of the full potential for NCIs made by backbone atoms. Most commonly, backbone‐carbonyl oxygen atoms located within α‐helices and β‐sheets are depicted as making a single hydrogen bond. However, there are two lone pairs of electrons to be satisfied for each of these atoms. To explore this, we used operational geometric definitions to generate an inventory of NCIs for backbone‐carbonyl oxygen atoms from a set of high‐resolution protein structures and associated molecular‐dynamics simulations in water. We included more‐recently appreciated, but weaker NCIs in our analysis, such as n→π* interactions, Cα‐H bonds and methyl‐H bonds. The data demonstrate balanced, dynamic systems for all proteins, with most backbone‐carbonyl oxygen atoms being satisfied by two NCIs most of the time. Combinations of NCIs made may correlate with secondary structure type, though in subtly different ways from traditional models of α‐ and β‐structure. In addition, we find examples of under‐ and over‐satisfied carbonyl‐oxygen atoms, and we identify both sequence‐dependent and sequence‐independent secondary‐structural motifs in which these reside. Our analysis provides a more‐detailed understanding of these contributors to protein structure and stability, which will be of use in protein modeling, engineering and design.

Molecularly Tuning the Radicaloid N-H···O═C Hydrogen Bond

Substituent effects on the open shell N-H···O═C hydrogen-bond has never been reported. This study examines how 12 functional groups composed of electron donating groups (EDG), halogen atoms and electron withdrawing groups (EWG) affect the N-H···O═C hydrogen-bond properties in a six-membered cyclic model system of O═C(Y)-CH═C(X)N-H. It is found that group effects on this open shell H-bonding system are significant and have predictive trends when X = H and Y is varied. When Y is an EDG, the N-H···O═C hydrogen-bond is strengthened; and when Y is an EWG, the bond is weakened; whereas the variation in electronic properties of X group do not exhibit a significant impact upon the hydrogen bond strength. The structural impact of the stronger N-H···O═C hydrogen-bond are (1) shorter H and O distance, r(H···O) and (2) a longer N-H bond length, r(NH). The stronger N-H···O═C hydrogen-bond also acts to pull the H and O in toward one another which has an effect on the bond angles. Our findings show that there is a linear relationship between hydrogen-bond angle and N-H···O═C hydrogen-bond energy in this unusual H-bonding system. In addition, there is a linear correlation of the r(H···O) and the hydrogen bond energy. A short r(H···O) distance corresponds to a large hydrogen bond energy when Y is varied. The observed trends and findings have been validated using three different methods (UB3LYP, M06-2X, and UMP2) with two different basis sets.

Microwave and Quantum Chemical Study of Intramolecular Hydrogen Bonding in 2-Propenylhydrazine (H2C═CHCH2NHNH2)

The microwave spectrum of 2-propenylhydrazine (H2C═CHCH2NHNH2) was studied in the 12-61 and 72-123 GHz spectral regions. A variety of intramolecular hydrogen bonds between one or more of the hydrogen atoms of the hydrazino group and the π-electrons are possible for this compound. Assignments of the spectra of four conformers, all of which are stabilized with intramolecular hydrogen bonds are reported. One hydrogen bond exists in two of these conformers, whereas the π-electrons are shared by two hydrogen atoms in the two other rotamers. Vibrationally excited-state spectra were assigned for three of the four conformers. The internal hydrogen bonds are weak, probably in the 3-6 kJ/mol range. A total of about 4400 transitions were assigned for these four forms. The microwave work was guided by quantum chemical calculations at the B3LYP/cc-pVTZ and CCSD/cc-pVTZ levels of theory. These calculations indicated that as many as 18 conformers may exist for 2-propenylhydrazine and 11 of these have either one or two intramolecular hydrogen bonds. The four conformers detected in this work are among the rotamers with the lowest CCSD electronic energies. The CCSD method predicts rotational constants that are very close to the experimental rotational constants. The B3LYP calculations yielded quartic centrifugal distortion constants that deviated considerably from their experimental counterparts in most cases. The calculation of vibration-rotation constants and sextic centrifugal distortion constants by the B3LYP method were generally found to be in poor agreement with the corresponding experimental constants.

Structure of Amido Pyridinium Betaines: Persistent Intermolecular C-H⋅⋅⋅N Hydrogen Bonding in Solution

A hydrogen bond of the type C-H⋅⋅⋅X (X=O or N) is known to influence the structure and function of chemical and biological systems in solution. C-H⋅⋅⋅O hydrogen bonding in solution has been extensively studied, both experimentally and computationally, whereas the equivalent thermodynamic parameters have not been enumerated experimentally for C-H⋅⋅⋅N hydrogen bonds. This is, in part, due to the lack of systems that exhibit persistent C-H⋅⋅⋅N hydrogen bonds in solution. Herein, a class of molecule based on a biologically active norharman motif that exhibits unsupported intermolecular C-H⋅⋅⋅N hydrogen bonds in solution has been described. A pairwise interaction leads to dimerisation to give bond strengths of about 7 kJ mol^-1 per hydrogen bond, which is similar to chemically and biologically relevant C-H⋅⋅⋅O hydrogen bonding. The experimental data is supported by computational work, which provides additional insight into the hydrogen bonding by consideration of electrostatic and orbital interactions and allowed a comparison between calculated and extrapolated NMR chemical shifts.

Accurate thermodynamic properties of gas phase hydrogen bonded complexes

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

Structure dependent toxicity of lignin phenolics and PEG detoxification in VHG ethanol fermentation

The inhibitory effects of phenolic compounds on ethanol fermentation were alleviated by intermolecular hydrogen bond of phenolic compounds with PEGs.

Highly stable naphthalene core based novel cleft-shaped strain molecule: influence of intermolecular H-bonding architectures

High thermal stability of a 8 membered naphthalene core based fused nitrogen bridged 1,5-dioxocin is found to be due to the coexistence of several weak interactions. Catalytic property of this molecule for a condensation reaction is also explored.

Understanding the anion–π interactions with tetraoxacalix[2]arene[2]triazine

The geometries of four anion–π complexes,1·X⁻(X⁻= SCN⁻, NO₃⁻, BF₄⁻, and PF₆⁻) were optimized using the extended ONIOM (XO) method with a high level (H) = ωB97X-D/6-31+G(d) and low level (L) = PM6. Then, the bonding energies of1·X⁻were calculated with the XYG3 functional, and they follow the order of1·NO₃⁻>1·SCN⁻>1·BF₄⁻>1·PF₆⁻.

Characterization of N⋯O non-covalent interactions involving σ-holes: “electrostatics” or “dispersion”

Exploring the possibility of formation of pnicogen bonds or chalcogen bonds by utilizing the σ-holes present on nitrogen and oxygen atoms in per-halo substituted complexes.

The unique functional role of the C–H⋯S hydrogen bond in the substrate specificity and enzyme catalysis of type 1 methionine aminopeptidase

Unique C–H⋯S hydrogen bonding interactions allow nature to attain recognition specificity between molecular interfaces where there is no apparent scope for classical hydrogen bonding or polar interactions.

Experimental and computational analysis of supramolecular motifs involving Csp2(aromatic)–F and CF3groups in organic solids

Structural motif by C_sp2–F and CF₃group have been identified and investigated by the PIXEL method and QTAIM approach.

Bis-(benzothiazol-2-yl)-amines and their metal amides: a structural comparison in the solid state

A series of functionalised bis-(benzothiazol-2-yl)-amine ligands and the related dimethylaluminium amides were synthesised and characterised. The solid state structural comparison reveals various coordination motifs, specific folding parameters and hydrogen bonding patterns in detail and guide the way to future Janus head ligand design.

Microwave spectroscopic and theoretical investigations of the strongly hydrogen bonded hexafluoroisopropanol···water complex

This paper reports microwave spectroscopic and theoretical investigations on the interaction of water with hexafluoroisopropanol (HFIP). The HFIP monomer can exist in two conformations, antiperiplanar (AP) and synclinical (SC). The former is about 5 kJ mol(-1) more stable than the latter. Theoretical calculations predicted three potential minima for the complex, two having AP and one having SC conformations. Though, the binding energy for the HFIP(SC)···H2O turned out to be larger than that for the other two conformers having HFIP in the AP form, the global minimum for the complex in the potential energy hypersurface had HFIP in the AP form. Experimental rotational constants for four isotopologues measured using a pulsed nozzle Fourier transform microwave spectrometer, correspond to the global minimum in the potential energy hypersurface. The structural parameters and the internal dynamics of the complex could be determined from the rotational spectra of the four isotopologues. The global minimum has the HFIP(AP) as a hydrogen bond donor forming a strong hydrogen bond with H2O. To characterize the strength of the bonding and to probe the other interactions within the complex, atoms in molecules, non-covalent interaction index and natural bond orbital theoretical analyses have been performed.

Multifunctional Tricarbazolo Triazolophane Macrocycles: One-Pot Preparation, Anion Binding, and Hierarchical Self-Organization of Multilayers

Programming the synthesis and self-assembly of molecules is a compelling strategy for the bottom-up fabrication of ordered materials. To this end, shape-persistent macrocycles were designed with alternating carbazoles and triazoles to program a one-pot synthesis and to bind large anions. The macrocycles bind anions that were once considered too weak to be coordinated, such as PF6 (-) , with surprisingly high affinities (β2 =10(11)  M(-2) in 80:20 chloroform/methanol) and positive cooperativity, α=(4 K2 /K1 )=1200. We also discovered that the macrocycles assemble into ultrathin films of hierarchically ordered tubes on graphite surfaces. The remarkable surface-templated self-assembly properties, as was observed by using scanning tunneling microscopy, are attributed to the complementary pairing of alternating triazoles and carbazoles inscribed into both the co-facial and edge-sharing seams that exist between shape-persistent macrocycles. The multilayer assembly is also consistent with the high degree of molecular self-association observed in solution, with self-association constants of K=300 000 M(-1) (chloroform/methanol 80:20). Scanning tunneling microscopy data also showed that surface assemblies readily sequester iodide anions from solution, modulating their assembly. This multifunctional macrocycle provides a foundation for materials composed of hierarchically organized and nanotubular self-assemblies.

Molecular Solution Behaviour of an Intermediate Biofuel Feedstock: Acetone-Butanol-Ethanol (ABE)

Mixtures of acetone, butanol, and ethanol (ABE) are common intermediate products in the production of biofuels via biomass fermentation. Their separation to yield, for example, bio-butanol, is still difficult due to the lack of a fundamental understanding of these mixtures at the molecular level. In order to bridge this gap, a detailed analysis of characteristic features of the vibrational spectrum is carried out. A systematic study of the binary solutions of acetone with ethanol and butanol does not only reveal a universal behaviour at the molecular level when acetone is mixed with short-chain alcohols, it also shows that the phenomena at a length scale between the molecules and in the macroscopic solution need to be taken into account to understand the structure-property relationships. The size of self-associated molecule clusters seems to determine whether or not a system exhibits an azeotrope. When a second alcohol is added to an acetone/alcohol solution, no additional non-idealities are induced, which is advantageous for modelling ternary ABE mixtures and for improving their processing in the production of biofuels.

Gas Phase Detection of the NH-P Hydrogen Bond and Importance of Secondary Interactions

We have observed the NH···P hydrogen bond in a gas phase complex. The bond is identified in the dimethylamine-trimethylphosphine complex by a red shift of the fundamental NH-stretching frequency observed using Fourier transform infrared spectroscopy (FT-IR). On the basis of the measured NH-stretching frequency red shifts, we find that P is a hydrogen bond acceptor atom similar in strength to S. Both are stronger acceptors than O and significantly weaker acceptors than N. The hydrogen bond angle, ∠NHP, is found to be very sensitive to the functional employed in density functional theory (DFT) optimizations of the complex and is a possible parameter to assess the quality of DFT functionals. Natural bonding orbital (NBO) energies and results from the topological methods atoms in molecules (AIM) and noncovalent interactions (NCI) indicate that the sensitivity is caused by the weakness of the hydrogen bond compared to secondary interactions. We find that B3LYP favors the hydrogen bond and M06-2X favors the secondary interactions leading to under- and overestimation, respectively, of the hydrogen bond angle relative to a DF-LCCSD(T)-F12a calculated angle. The remaining functionals tested, B3LYP-D3, B3LYP-D3BJ, CAM-B3LYP, and ωB97X-D, as well as MP2, show comparable contributions from the hydrogen bond and the secondary interactions and are close to DF-LCCSD(T)-F12a results.

Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding

One hundred complexes have been investigated exhibiting D-X···A interactions, where X = H, Cl or Li and DX is the 'X bond' donor and A is the acceptor. The optimized structures of all these complexes have been used to propose a generalized 'Legon-Millen rule' for the angular geometry in all these interactions. A detailed Atoms in Molecules (AIM) theoretical analysis confirms an important conclusion, known in the literature: there is a strong correlation between the electron density at the XA bond critical point (BCP) and the interaction energy for all these interactions. In addition, we show that extrapolation of the fitted line leads to the ionic bond for Li-bonding (electrostatic) while for hydrogen and chlorine bonding, it leads to the covalent bond. Further, we observe a strong correlation between the change in electron density at the D-X BCP and that at the X···A BCP, suggesting conservation of the bond order. The correlation found between penetration and electron density at BCP can be very useful for crystal structure analysis, which relies on arbitrary van der Waals radii for estimating penetration. Various criteria proposed for shared- and closed-shell interactions based on electron density topology have been tested for H/Cl/Li bonded complexes. Finally, using the natural bond orbital (NBO) analysis it is shown that the D-X bond weakens upon X bond formation, whether it is ionic (DLi) or covalent (DH/DCl) and the respective indices such as ionicity or covalent bond order decrease. Clearly, one can think of conservation of bond order that includes ionic and covalent contributions to both D-X and X···A bonds, for not only X = H/Cl/Li investigated here but also any atom involved in intermolecular bonding.

Insights into the Nature of Anesthetic-Protein Interactions: An ONIOM Study

Anesthetics have been employed widely to relieve surgical suffering, but their mechanism of action is not yet clear. For over a century, the mechanism of anesthesia was previously thought to be via lipid bilayer interactions. In the present work, a rigorous three-layer ONIOM(M06-2X/6-31+G*:PM6:AMBER) method was utilized to investigate the nature of interactions between several anesthetics and actual protein binding sites. According to the calculated structural features, interaction energies, atomic charges, and electrostatic potential surfaces, the amphiphilic nature of anesthetic-protein interactions was demonstrated for both inhalational and injectable anesthetics. The existence of hydrogen and halogen bonding interactions between anesthetics and proteins was clearly identified, and these interactions served to assist ligand recognition and binding by the protein. Within all complexes of inhalational or injectable anesthetics, the polarization effects play a dominant role over the steric effects and induce a significant asymmetry in the otherwise symmetric atomic charge distributions of the free ligands in vacuo. This study provides new insight into the mechanism of action of general anesthetics in a more rigorous way than previously described. Future rational design of safer anesthetics for an aging and more physiologically vulnerable population will be predicated on this greater understanding of such specific interactions.

Sequence-Dependent Conformational Heterogeneity and Proton-Transfer Reactivity of the Fluorescent Guanine Analogue 6-Methyl Isoxanthopterin (6-MI) in DNA

The local conformations of individual nucleic acid bases in DNA are important components in processes fundamental to gene regulation. Fluorescent nucleic acid base analogues, which can be substituted for natural bases in DNA, can serve as useful spectroscopic probes of average local base conformation and conformational heterogeneity. Here we report excitation-emission peak shift (EES) measurements of the fluorescent guanine (G) analogue 6-methyl isoxanthoptherin (6-MI), both as a ribonucleotide monophosphate (NMP) in solution and as a site-specific substituent for G in various DNA constructs. Changes in the peak positions of the fluorescence spectra as a function of excitation energy indicate that distinct subpopulations of conformational states exist in these samples on time scales longer than the fluorescence lifetime. Our pH-dependent measurements of the 6-MI NMP in solution show that these states can be identified as protonated and deprotonated forms of the 6-MI fluorescent probe. We implement a simple two-state model, which includes four vibrationally coupled electronic levels to estimate the free energy change, the free energy of activation, and the equilibrium constant for the proton transfer reaction. These parameters vary in single-stranded and duplex DNA constructs, and also depend on the sequence context of flanking bases. Our results suggest that proton transfer in 6-MI-substituted DNA constructs is coupled to conformational heterogeneity of the probe base, and can be interpreted to suggest that Watson-Crick base pairing between 6-MI and its complementary cytosine in duplex DNA involves a "low-barrier-hydrogen-bond". These findings may be important in using the 6-MI probe to understand local base conformational fluctuations, which likely play a central role in protein-DNA and ligand-DNA interactions.

Heterogeneity and Specificity of Nanoscale Adhesion Forces Measured between Self-Assembled Monolayers and Lignocellulosic Substrates: A Chemical Force Microscopy Study

Lack of fundamental understanding of cellulase interactions with different plant cell wall components during cellulose saccharification hinders progress toward achieving an economic production of biofuels from renewable plant biomass. Here, chemical force microscopy (CFM) was utilized to quantify the interactions between two surfaces that model either hydrophilic or hydrophobic functional groups of cellulases and a set of lignocellulosic substrates prepared through Kraft, sulfite, or organosolv pulping with defined chemical composition. The measured forces were then decoupled into specific and nonspecific components using the Poisson statistical approach. Heterogeneities in the distributions of forces as a function of the pretreatment method were mapped. Our results showed that hydrophobic domains and chemical moieties involved in hydrogen bonding and polar interactions were homogeneously distributed on all substrates but with distribution densities that varied with the type of the pretreatment method used to prepare substrates. In addition, we showed that increasing surface lignin coverage increased the heterogeneity of the substrates. When forces were decoupled, our results indicated that xylan reduced the strength of hydrogen bonding between the hydrophilic model surface and substrates. Permanent dipole-dipole interactions dominated the adhesion of the hydrophilic model surface to lignosulfonates, whereas hydrophobic interactions facilitated the adhesion of the hydrophobic model surface to Kraft lignin. We further showed that the structure of lignin determines the type of forces that dominate lignocellulosic interactions with other surfaces. Our findings suggest that nonproductive binding of cellulases to lignocellulosic biomass can be reduced by altering the hydrophobicity and/or chemical moieties involved in the polar interactions and by utilizing organosolv as a pretreatment method.

A systematic structural study of halogen bonding versus hydrogen bonding within competitive supramolecular systems

As halogen bonds gain prevalence in supramolecular synthesis and materials chemistry, it has become necessary to examine more closely how such interactions compete with or complement hydrogen bonds whenever both are present within the same system. As hydrogen and halogen bonds have several fundamental features in common, it is often difficult to predict which will be the primary interaction in a supramolecular system, especially as they have comparable strength and geometric requirements. To address this challenge, a series of molecules containing both hydrogen- and halogen-bond donors were co-crystallized with various monotopic, ditopic symmetric and ditopic asymmetric acceptor molecules. The outcome of each reaction was examined using IR spectroscopy and, whenever possible, single-crystal X-ray diffraction. 24 crystal structures were obtained and subsequently analyzed, and the synthon preferences of the competing hydrogen- and halogen-bond donors were rationalized against a background of calculated molecular electrostatic potential values. It has been shown that readily accessible electrostatic potentials can offer useful practical guidelines for predicting the most likely primary synthons in these co-crystals as long as the potential differences are weighted appropriately.

Tunable dipole induced hydrogen bonds between a hydrogen molecule and alkali halides

Hydrogen bonding (HB) systems are known to be X-H∙∙∙Y type complexes, which are called conventional HB systems if the X and Y are strongly electronegative atoms such as O, N and halides or unconventional systems if the X is replaced by C. In this study, we devise a new dipole-induced HB that is formed between a hydrogen molecule and an alkali halide using ab initio calculations. The HB is depicted as H-H∙∙∙Y-M, in which MY are alkali halides. Analysis of the possible structures and properties of the proposed compounds, including their geometries, frequencies, bond strength, and natural charge distribution, as well as a topological analysis of electronic density, shows that the large dipole moment of the Y-M molecule is responsible for the generation of the proposed HB. We also find that the strength of HB can be tuned by adopting MY with various polarities. We hope that our findings could provide a new insight into HB.

Topological insights into the 1/1 diacetyl/water complex gained using a new methodological approach

The 1/1 diacetyl/water complex is of atmospheric relevance. Previous experimental and theoretical studies have focused on two isomeric forms, and geometry optimizations were carried out on them. Herein, we propose a six-step methodological approach based on topological properties to search for and characterize all of the isomeric forms of the 1/1 noncovalent diacetyl/water complex: (1) a molecular electrostatic potential (MESP) study to get an overview of the V min and V max regions on the molecular surfaces of the separate molecules (diacetyl and water); (2) a topological (QTAIM and ELF) study allowing thorough characterization of the electron densities (QTAIM) and irreducible ELF basins of the separate molecules; (3) full optimization of the predicted structures based on the interaction between complementary reaction sites; (4) energetic characterization based on a symmetry-adapted perturbation theory (SAPT) analysis; (5) topological characterization of the optimized complexes; (6) analysis of the complexes in terms of orbital overlaps (natural bond orbitals, NBO analysis). Using this approach, in addition to achieving the topological characterization of the two isomeric forms already reported, a third possible isomer was identified and characterized. Graphical Abstract Topological tools to study monohydrated complexes.

Hydrogen bonding in ionic liquids

Ionic liquids (IL) and hydrogen bonding (H-bonding) are two diverse fields for which there is a developing recognition of significant overlap. Doubly ionic H-bonds occur when a H-bond forms between a cation and anion, and are a key feature of ILs. Doubly ionic H-bonds represent a wide area of H-bonding which has yet to be fully recognised, characterised or explored. H-bonds in ILs (both protic and aprotic) are bifurcated and chelating, and unlike many molecular liquids a significant variety of distinct H-bonds are formed between different types and numbers of donor and acceptor sites within a given IL. Traditional more neutral H-bonds can also be formed in functionalised ILs, adding a further level of complexity. Ab initio computed parameters; association energies, partial charges, density descriptors as encompassed by the QTAIM methodology (ρBCP), qualitative molecular orbital theory and NBO analysis provide established and robust mechanisms for understanding and interpreting traditional neutral and ionic H-bonds. In this review the applicability and extension of these parameters to describe and quantify the doubly ionic H-bond has been explored. Estimating the H-bonding energy is difficult because at a fundamental level the H-bond and ionic interaction are coupled. The NBO and QTAIM methodologies, unlike the total energy, are local descriptors and therefore can be used to directly compare neutral, ionic and doubly ionic H-bonds. The charged nature of the ions influences the ionic characteristics of the H-bond and vice versa, in addition the close association of the ions leads to enhanced orbital overlap and covalent contributions. The charge on the ions raises the energy of the Ylp and lowers the energy of the X-H σ* NBOs resulting in greater charge transfer, strengthening the H-bond. Using this range of parameters and comparing doubly ionic H-bonds to more traditional neutral and ionic H-bonds it is clear that doubly ionic H-bonds cover the full range of weak through to very strong H-bonds.