Hydrogen Bond-like Interactions Research Articles

Silicon rib waveguide with palladium coated gold nanorods overlayer for hexane and N-methylaniline detection

The adsorption of hexane and N-methylaniline was investigated by on-chip vibrational spectroscopy. The interaction with the Pd surface significantly perturbs the vibrational modes of hexane. Near-infrared absorption spectroscopy on the waveguide detected a redshifted CH stretching vibration. We showed that while rapid evaporation of one component may occur, the modification facilitates the sensing for large molecules and mixtures of substances. Rib waveguides were modified with palladium to exhibit an enhanced electromagnetic field effect due to the electrostatic interaction of Pd and hydrogen, showing the drop in the amine overtone absorption of 7.6 dB and the overtone related to the bond of carbon to hydrogen of 6.8 dB. The absorption of hexane bonds in water is 5.5 dB. The obtained values are 100 times higher than those predicted by the electromagnetic simulator for pure rib waveguides. This may be explained by CH bonds in hexane that can be activated through a hydrogen bond-like interaction with metal substrates. This achievement holds promising potential for advancing hexane and N-Methylailine detection and analysis technologies, with implications for diverse applications in various industries, such as environmental monitoring, industrial processes, and safety measures.

Exploring the influence of bis-phosphine ligands on lanthanide complexes: A DFT study

This study employs density functional theory (DFT) calculation to investigate the bis-phosphine ligands interaction with lanthanide ions (La3+, Nd3+, Eu3+, Er3+ and Lu3+). Two distinct bridging modes are explored between two phosphine ligands: pyridine and methylene functional groups. The aim is to understand the structural, thermochemical, spectroscopic, and orbital properties of the bis-phosphine-Ln3+ complexes and compare the effects of different bridging modes. It is observed that bis-phosphine ligands form the most stable complexes with Er3+ and the least stable complexes with La3+, as evidenced by interaction energies, Gibb’s free energies and electrophilicity index values. Pyridine-bridged ligands form more stable complexes than methylene-bridged ligands, which is consistent with charge population analysis. Reduced density gradient analysis indicates the presence of strong hydrogen bond-like interactions between lanthanide ions and oxygen/nitrogen atoms of bis-phosphine complexes. Infrared spectra simulations reveal that Er3+ forms stronger bonds with oxygen atoms of bis-phosphine ligands than other lanthanide ions.

The Impact of the Complexing Cation on the Sensitivity of the Collisional-Induced Dissociation Spectra to Fatty Acid Position for a Set of YXY/YYX-type Triglycerides.

The development of an automated platform for the positional analysis of triglycerides based on electrospray tandem mass spectrometry continues to be pursued. This work compares the positional sensitivities of the collisional-induced dissociation spectra for a representative set of YXY/YYX triglycerides using ammonium, silver, sodium and lithium as complexing agents. A set of triglycerides were synthesized and analyzed by electrospray tandem mass spectrometry using an ion trap mass spectrometer. Using different salt additives, the product ion spectra of the corresponding parent ions for twelve systems of the form YXY/YYX, where Y and X represent C16:0 , C18:1(c-9), C18:2(cc-9,12) and C20:4(cccc-5,8,11,14) , were collected. The data was used to prepare two-point calibration plots for each of the twelve positional isomer systems using each of the four complexing agents. The positional sensitivities for all twelve positional isomer systems were robust for both the sodium and lithium TAG adducts. The CID data for both the sodium and lithium TAG adducts are much less sensitive to the degree of unsaturation and double bond position of the fatty acids constituents than the CID data for the ammonium adducts. Using sodium or lithium TAG adducts may be advantageous for the development of an accurate predictive model for performing positional analysis of complex TAG mixtures based on electrospray tandem mass spectrometry. Ammonium adducts are likely complicated by the ability of the ammonium ion to provide extra stability to some parent ions through hydrogen bond-like interactions.

Influences on the stability of collagen triple-helix

Collagen forms a triple helix structure which consists of three tightly coiled polyproline II-type (PPII) strands with the repeating amino acid motif Xaa-Yaa-Gly, where Xaa and Yaa are often proline (Pro) and hydroxproline (Hyp), respectively. The thermal and mechanical stability of the collagen triple-helix is a complex balance between several factors, e.g. sterical influences of substituents, stereoelectronic effects, or interstrand interactions. On the basis of computational studies, we have analyzed the influence of these effects and demonstrate that even comparatively small effects, like the stereoelectronic gauche-effect, and intramolecular hydrogen-bonding can have an impact on the triple-helix stability. In addition, our results suggest that hydrogen bond-like interactions perpendicular to the helix axis increase the stiffness of collagen. Our studies provide a deeper insight into the structure-directing factors in collagenous materials and will help to improve the synthesis of collagen-like biomaterials.

Interaction of Nucleobases with Wrinkled Graphene Surface: Dispersion Corrected DFT and AFM Studies

Graphene–nucleobase interaction is gaining importance due to its possible therapeutic applications. The dispersion interaction plays a major role in stacked aromatic compounds, such as graphene with amino acids or nucleobases. We have carried out detailed quantum chemical calculations of complexes of nanographene sheets and the nucleobases of DNA and RNA using dispersion corrected density functional theory. Binding energies show a trend as observed earlier by different theoretical and experimental measurements. However, in our present investigation, the optimized structures of the complex as well as isolated graphene show significant curvature, similar features are also observed by our Atomic Force Microscopic studies. Analysis of Natural Bond Orbital charges indicates the possibility of weak hydrogen bond-like interactions involving pyramidal amino groups of the nucleobases and π-center of the nanographene.

Impact of ligands on CO2 adsorption in metal-organic frameworks: First principles study of the interaction of CO2 with functionalized benzenes. I. Inductive effects on the aromatic ring

Intermolecular interactions between the CO(2) molecule and a range of functionalized aromatic molecules have been investigated using density functional theory. The work is directed toward the design of linker molecules which could form part of new metal-organic framework materials with enhanced affinity for CO(2) adsorption at low pressure. Two classes of substituted benzene molecules were considered: (i) with halogen substituents (tetrafluoro-, chloro-, bromo-, and dibromobenzene) and (ii) with methyl substituents (mono-, di-, and tetramethylbenzene). In the benzene-CO(2) complex, the main interaction is between the delocalized pi aromatic system and the molecular quadrupole of CO(2). Halogen substituents have an electron-withdrawing effect on the ring which destabilizes the pi-quadrupole interaction. Weak "halogen-bond" and hydrogen bondlike interactions partially compensate for this, but not to the extent that any significant enhancement of the intermolecular binding energy is observed. Methyl groups, on the other hand, have a positive inductive effect which strengthens the CO(2)-aromatic interaction by up to 3 kJ mol(-1) in the case of tetramethylbenzene. Weak hydrogen bondlike interactions with methyl H also contribute to the stability of the complexes.

Experimental and Theoretical Study of the Coordination of 1,2,4-Triazolato, Tetrazolato, and Pentazolato Ligands to the [K(18-crown-6)]+ Fragment

Treatment of 3,5-diisopropyltriazole, 3,5-diphenyltriazole, 3,5-di-3-pyridyltriazole, phenyltetrazole, pyrrolidinyltetrazole, or tert-butyltetrazole with equimolar quantities of potassium hydride and 18-crown-6 in tetrahydrofuran at ambient temperature led to slow hydrogen evolution and formation of (3,5-diisopropyl-1,2,4-triazolato)(18-crown-6)potassium (88%), (3,5-diphenyl-1,2,4-triazolato)(tetrahydrofuran)(18-crown-6)potassium (87%), (3,5-di-3-pyridyl-1,2,4-triazolato)(18-crown-6)potassium (81%), (phenyltetrazolato)(18-crown-6)potassium (94%), (pyrrolidinyltetrazolato)(18-crown-6)potassium (90%), and (tert-butyltetrazolato)(18-crown-6)potassium (94%) as colorless crystalline solids. (1,2,4-Triazolato)(18-crown-6)potassium was isolated as a hemi-hydrate in 81% yield upon treatment of 1,2,4-triazole with potassium metal in tetrahydrofuran. The X-ray crystal structures of these new complexes were determined, and the solid-state structures consist of the nitrogen heterocycles bonded to the (18-crown-6)potassium cationic fragments with eta2-bonding interactions. In addition, (3,5-diphenyl-1,2,4-triazolato)(tetrahydrofuran)(18-crown-6)potassium has one coordinated tetrahydrofuran ligand on the same face as the 3,5-diphenyl-1,2,4-triazolato ligand, while (3,5-di-3-pyridyl-1,2,4-triazolato)(18-crown-6)potassium forms a polymeric solid through coordination of the distal 3-pyridyl nitrogen atoms to the potassium ion on the face opposite the 1,2,4-triazolato ligand. The solid-state structures of the new complexes show variable asymmetry in the potassium-nitrogen distances within the eta2-interactions and also show variable bending of the heterocyclic C2N3 and CN4 cores toward the best plane of the 18-crown-6 ligand oxygen atoms. Molecular orbital and natural bond order calculations were carried out at the B3LYP/6-311G(d,p) level of theory on the model complex, (phenyltetrazolato)(18-crown-6)potassium, and demonstrate that the asymmetric potassium-nitrogen distances and bending of the CN4 core toward the 18-crown-6 ligand are due to hydrogen bond-like interactions between filled nitrogen-based orbitals and carbon-hydrogen sigma orbitals on the 18-crown-6 ligands. Calculations carried out on the model pentazolato complex (pentazolato)(18-crown-6)potassium predict a structure in which the pentazolato ligand N5 core is bent by 45 degrees toward the best plane of the 18-crown-6 oxygen atoms. Such bending is induced by the formation of intramolecular nitrogen-hydrogen-carbon hydrogen bonds. Examination of the solid-state structures of the new complexes reveals many intramolecular and intermolecular nitrogen-hydrogen distances of < or =3.0 A which support the presence of nitrogen-hydrogen-carbon hydrogen bonds.

Lattice polymers with hydrogen bondlike interactions

We study the phase behavior of two lattice polymer models (self-avoiding walks) incorporating attractive short-range interactions between parallel chain sections, attempting to mimick hydrogen bonding between monomers. The investigation is carried out in the framework of the Bethe approximation on a hypercubic lattice. The former model, which includes attraction between parallel sections longer than one chain segment, has been recently studied in full detail in the two-dimensional case, by means of accurate numerical transfer matrix techniques, and displays a first-order transition from a swollen (“coil”) state to a collapsed ordered (“solid”) state. Our investigation on this model is mainly meant to show that the Bethe approximation is able to recover such a behavior, and to extend the result to three dimensions. The latter model is similar, but takes into account attractive interactions also between one segment long parallel sections, which have no reason to be neglected in principle. We obtain, both in two and three dimensions, two phase transitions: An ordinary theta-collapse from the coil state to an isotropic compact (“globule”) state, and a first-order transition from the globule to the solid phase. Such results are compared with those of previously investigated polymer models, and their relevance to describe the formation of protein secondary structure is also briefly discussed.

Ab initio and DFT conformational analysis of selected flavones: 5,7-dihydroxyflavone (chrysin) and 7,8-dihydroxyflavone

Ab initio and DFT conformational analysis was performed on the flavone derivatives chrysin (5,7-dihydroxyflavone; 2-phenyl-5,7-dihydroxy-4H-1-benzopyran-4-one) and 7,8-dihydroxyflavone (2-phenyl-7,8-dihydroxy-4H-1-benzopyran-4-one). The structural features required for optimal stabilization in each molecule were identified. It was discovered that sparsely placed hydroxyl groups, particularly with hydrogen bond-like interactions, resulted in lowering the potential energy minimum for the molecules. It was also noted that one of the factors capable of destroying co-planarity was steric interference between closely placed functional groups across the phenyl and the benzo-γ-pyrane ring. Studies performed on the radical forms of the flavonoids, however, showed that the unpaired electron is confined only to the benzo-γ-pyrane ring, and not delocalized across the phenyl ring.Key words: flavonoid, flavone, chrysin, ab initio conformational analysis, anti-oxidant, free radical, 5,7-dihydroxy flavone, 7,8-dihydroxyflavone.

Surface color centers as novel hydrogen bond acceptors

In recent combined electron paramagnetic resonance and infrared spectroscopic studies a very specific interaction between surface OH groups and surface color centers was observed on nanometer-sized MgO particles. The positions of the respective OH stretching bands point to hydrogen bond-like interactions. On the other hand, the bandwidths indicate that the color center electron as proton acceptor is strongly localized.

Infrared C–D Stretching and 2H NMR Spectra of Isopropyl-2-d 1-(p-Substituted Phenyl)ethyl Ketones. Evidence for the Hydrogen Bond-Like Interaction between C–D Group and Aromatic π-Electrons

Abstract Isopropyl-2-d 1-(p-X-phenyl)ethyl ketones (where, X=H, NO2, Br, Cl, C2H5, CH3, and NH2) were shown to have two absorption bands in the C–D stretching region. The absorption band at the higher frequency (ca. 2177 cm−1) is assigned to the C–D···π approached conformer, and the high frequency shift is ascribed to the effect of steric compression. Weak C–D···π hydrogen bond was shown to occur by the measurement of the substituent effect on the formation constant and the relative enthalpy of the C–D···π approached conformer.

EELS analysis of the low temperature phase of ethylene chemisorbed on Pd(111)

The chemisorption of C 2H 4 and C 2D 4 on Pd(111) at 150 K has been studied by high resolution electron energy loss spectroscopy. Analysis of the vibrational spectra indicates that (i) C 2H 4 is more weakly bound on Pd(111) than on Ni(111) and Pt(111) and (ii) softened and broadened CH stretching frequencies suggest hydrogen bond-like interactions between the molecule and the metal surface.

Eels analysis of the low temperature phase of ethylene chemisorbed on Pd(111)

The chemisorption of C 2H 4 and C 2D 4 on Pd(111) at 150 K has been studied by high resolution electron energy loss spectroscopy. Analysis of the vibrational spectra indicates that (i) C 2H 4 is more weakly bound on Pd(111) than on Ni(111) and Pt(111) and (ii) softened and broadened CH stretching frequencies suggest hydrogen bond-like interactions between the molecule and the metal surface.