Quantum Study on the Hydrogen Bonding Interaction of Luteolin-（CH_3OH）_n

The optimized geometries and vibration frequencies of luteolin,methanol and luteolin-(CH3OH)n complexes have been investigated by density functional theory using B3LYP method.Four stable luteolin-CH3OH complexes,six stable luteolin-(CH3OH)2 complexes and four stable luteolin-(CH3OH)3 complexes have been obtained.The theories of atoms in molecules(AIM) and natural bond orbital(NBO) have been used to analyze the hydrogen bonds of these compounds,and their interaction energies corrected by basis set superposition error are between-8.046 and-76.124 kJ/mol.The calculation results indicate strong hydrogen bonding interactions in the luteolin-(CH3OH)n complexes.Then the nuclear magnetic resonance(NMR) and electronic absorption spectrum of luteolin have been calculated,and the results are in agreement with the experimental data.     

Theoretical Study on the Structures and Properties of Hydrogen Bonding Complexes between Diazines and Water

Density functional theory B3LYP method and second-order Moller-Plesset perturbation theory MP2 method were employed to obtain the optimized geometries of the ground state and interaction energy for diazines and water complexes. The results show that the ground state complexes have strong hydrogen bonding interaction with -20.99, -16.73 and -15.31 kJ/mol after basis set superposition error and zero-point vibration energy correction for pyridazine-water, pyrimidine-water and pyrazine-water, respectively, and large red-shift for the symmetric H-O stretching vibration frequencies due to the formation of N…H-O hydrogen bond in the diazine-water complexes. The NBO analysis indicates that intermolecular charge transfer are 0.0316, 0.0255 and 0.0265 e respectively. In addition, the first singlet （n,n＊） vertical excitation energy of the monomer and the hydrogen bonding complexes between diazines and water was investigated by time-dependent density functional theory.     

Conformational Analysis and Study of Hydrogen Bonding of Iodobicycloheptanyl-N′-(trifluoromethanesulfonyl) Acetimidamides

Russian Journal of General Chemistry - Structure of iodobicycloheptanyl-N′-(trifluoromethanesulfonyl) acetimidamide epimers and its self-associates in crystal, solution and gas phase was...     

Exploring the Nature of Hydrogen Bonding between RNA and Proteins: A Comprehensive Analysis of RNA : Protein Complexes

A nonredundant dataset of ∼300 high (up to 2.5 Å) resolution X-ray structures of RNA : protein complexes were analyzed for hydrogen bonds between amino-acid residues and canonical ribonucleotides (rNs). The identified 17100 contacts were classified based on the identity (rA, rC, rG or rU) and interacting fragment (base, sugar, or ribose) of the rN, the nature (polar or nonpolar) and interacting moiety (main chain or side chain) of the amino-acid residue, as well as the rN and amino-acid atoms participating in the hydrogen bonding. 80 possible hydrogen-bonding combinations (4 (rNs)×20 (amino acids)) involve a wide variety of RNA and protein types and are present in multiple occurrences in almost all PDB files. Comparison with the analogously-selected DNA:protein complexes reveals that the absence of 2′-OH group in DNA mainly accounts for the differences in DNA:protein and RNA : protein hydrogen bonding. Search for intrinsically-stable base:amino acid pairs containing single or multiple hydrogen bonds reveals 37 unique pairs, which may act as well-defined RNA : protein interaction motifs. Overall, our work collectively analyzes the largest set of nucleic acid-protein hydrogen bonds to date, and therefore highlights several trends that may help frame structural rules governing the physiochemical characteristics of RNA : protein recognition.     

Effects of Hydrogen Bonding on the Transition Properties of Ethanol–Water Clusters: A TD-DFT Study

In this work, time-dependent density functional theory method was used to study the electronic transitions of hydrogen-bonded ethanol–water complexes Dimer-I, Dimer-II and Trimer. The intermolecular hydrogen bonds H₁···O₁ and O···H₂ were demonstrated by the optimized geometric structures of the three hydrogen-bonded ethanol–water complexes. It is demonstrated that the S₁-state electronic transitions for ethanol monomer and the hydrogen-bonded complex Dimer-I (through HB-I) should be of LE nature on the ethanol molecule, while those of complexes Dimer-II and Trimer should be of CT character from the hydrogen-bonded water molecule (through HB-II) to the ethanol moiety. The different electronic transition types should be the reasons for the tiny redshift of the S₁-state electronic energy for Dimer-I and the large blueshifts for Dimer-II and the Trimer compared with that of the ethanol monomer.     

TD-DFT Study on the Excited-State Hydrogen Bonding of the p-Cresol–NH3–H2O Complex

In this work, the time-dependent density functional theory (TD-DFT) method was used to study the electronic excited-state dynamics of the hydrogen-bonded p-Cresol–NH₃–H₂O complex. The intermolecular hydrogen bonds O₁–H₁···N and C–O₁···H₂ were demonstrated by the optimized geometric structure of the hydrogen-bonded p-Cresol–NH₃–H₂O complex. The infrared spectra (IR spectra) of the hydrogen-bonded p-Cresol–NH₃–H₂O complex in the ground and excited states were also calculated by using the density functional theory (DFT) and TD-DFT methods. It is demonstrated that hydrogen bond O₁–H₁···N can be strengthened while hydrogen bond C–O₁···H₂ is weakened upon photoexcitation to the S₁ state. The significant changes of the hydrogen bond from the calculated bond lengths in different electronic states can be observed. In addition, the spectral shifts of the stretching vibrational mode of the hydrogen-bonded O–H group in different electronic states are accounted for the hydrogen bond changes in the S₁ state too.     

Halogen Bonding： An AIM Analysis of the Weak Interactions

A series of complexes formed between halogen-containing molecules and ammonia have been investigated by means of the atoms in molecules （AIM） approach to gain a deeper insight into halogen bonding. The existence of the halogen bond critical points （XBCP） and the values of the electron density （Pb） and Laplacian of electron density （V2pb） at the XBCP reveal the closed-shell interactions in these complexes. Integrated atomic properties such as charge, energy, polarization moment, volume of the halogen bond donor atoms, and the corresponding changes （△） upon complexation have been calculated. The present calculations have demonstrated that the halogen bond represents different AIM properties as compared to the well-documented hydrogen bond. Both the electron density and the Laplacian of electron density at the XBCP have been shown to correlate well with the interaction energy, which indicates that the topological parameters at the XBCP can be treated as a good measure of the halogen bond strength In addition, an excellent linear relationship between the interatomic distance d（X…N） and the logarithm of Pb has been established.     

Photodegradation of Riboflavin under Alkaline Conditions: What Can Gas-Phase Photolysis Tell Us about What Happens in Solution?

The application of electrospray ionisation mass spectrometry (ESI-MS) as a direct method for detecting reactive intermediates is a technique of developing importance in the routine monitoring of solution-phase reaction pathways. Here, we utilise a novel on-line photolysis ESI-MS approach to detect the photoproducts of riboflavin in aqueous solution under mildly alkaline conditions. Riboflavin is a constituent of many food products, so its breakdown processes are of wide interest. Our on-line photolysis setup allows for solution-phase photolysis to occur within a syringe using UVA LEDs, immediately prior to being introduced into the mass spectrometer via ESI. Gas-phase photofragmentation studies via laser-interfaced mass spectrometry of deprotonated riboflavin, [RF − H]⁻, the dominant solution-phase species under the conditions of our study, are presented alongside the solution-phase photolysis. The results obtained illustrate the extent to which gas-phase photolysis methods can inform our understanding of the corresponding solution-phase photochemistry. We determine that the solution-phase photofragmentation observed for [RF − H]⁻ closely mirrors the gas-phase photochemistry, with the dominant m/z 241 condensed-phase photoproduct also being observed in gas-phase photodissociation. Further gas-phase photoproducts are observed at m/z 255, 212, and 145. The value of exploring both the gas- and solution-phase photochemistry to characterise photochemical reactions is discussed.     

On the Correlation between the Blue Shift of Hydrogen Bonding and the Proton Donor-Proton Acceptor Distance

It is demonstrated that in all types of hydrogen bonds (X—H…Y) there is a balance between the long-range attractive orbital interactions and short-range Pauli/nucleus repulsions. When the proton acceptor approaches the proton donor from distance, the hydrogen bonding energy becomes more negative at relatively large distance, goes through a minimum, and then starts to become less negative when the short-range repulsive forces come into effect.Meanwhile, the X--H bond length increases at relatively large distances, goes through a maximum and starts to shorten when the short-range repulsive forces come into effect. Whether the hydrogen bond is red or blue shifted is dictated by the energy minimum position. If at the energy minimum position the X—H bond length is shorter than that for the free monomer, the hydrogen bond is blue shifted and vice versa. Further studies demonstrate that the recent report about the correlation of C—H bond lengths with proton donor-acceptor distance in F3C—H…OH2 and F3C—H…Cl^- is not fully correct because the authors conducted an inappropriate comparison. Furthermore, it is shown for the first time that the Pauli/nucleus repulsion theory is applicable to the blue-shifted hydrogen bonds in the X—H…π complexes and the blue-shifted lithium bonds in the X—Li…Y complexes.     

Can Counter-Intuitive Halogen Bonding Be Coulombic?

We use the term “counter-intuitive” to describe an intermolecular interaction in which the electrostatic potentials of the interacting regions of the ground-state molecules have the same sign, both positive or both negative. In the present work, we consider counter-intuitive halogen bonding with nitrogen bases, in which both the halogen σ-hole and the nitrogen lone pair have negative potentials on their molecular surfaces. We show that these interactions can be treated as Coulombic despite the apparent repulsion between the ground-state molecules, provided that both electrostatics and polarization are explicitly taken into account. We demonstrate first that the energies of 20 counter-intuitive interactions with four nitrogen bases can be expressed very well in terms of just two molecular properties: the electrostatic potential of the halogen σ-hole and the average polarizability of the nitrogen base. Then we show that the same two properties can also represent the energies of an expanded data base that includes the 20 counter-intuitive plus an additional 20 weak and moderately-strong intuitive halogen bonding interactions (in which the σ-hole potentials are now positive).     

Multiple Hydrogen Bonding Enables the Self-Healing of Sensors for Human–Machine Interactions

Despite its widespread use in signal collection, flexible sensors have been rarely used in human–machine interactions owing to its indistinguishable signal, poor reliability, and poor stability when inflicted with unavoidable scratches and/or mechanical cuts. A highly sensitive and self-healing sensor enabled by multiple hydrogen bonding network and nanostructured conductive network is demonstrated. The nanostructured supramolecular sensor displays extremely fast (ca. 15 s) and repeatable self-healing ability with high healing efficiency (93 % after the third healing process). It can precisely detect tiny human motions, demonstrating highly distinguishable and reliable signals even after cutting–healing and bending over 20 000 cycles. Furthermore, a human–machine interaction system is integrated to develop a facial expression control system and an electronic larynx, aiming to control the robot to assist the patient's daily life and help the mute to realize real-time speaking.     

How Strong is Hydrogen Bonding to Amide Nitrogen?

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

Significance of Protein–Substrate Hydrogen Bonding for the Selectivity of P450-Catalysed Oxidations

P450_cin and P450_cam are bacterial cytochromes P450 that specifically hydroxylate bicyclic monoterpenes. Protein–substrate H bonding has been previously proposed as crucial in the selectivity of P450_cin oxidations, but not as essential for P450_cam. To examine the difference in importance of H bonds in these two model P450s, the P450-catalysed oxidation products from thiocamphor were compared. Surprisingly, both P450s oxidised thiocamphor predominantly to the corresponding S-oxides, in contrast to previous reports, and this is the first report of P450-catalysed sulfine generation from a thioketone. Additionally, the result emphasised the importance of the protein–substrate H bond to selectivity in both P450_cin and P450_cam. The H bonding in P450_cam was re-examined using camphane, another substrate for which the protein–substrate H bond is absent. The results indicated that both H bonding and hydrophobic interactions between substrate and protein play a role in selectivity. Interestingly, the protein–substrate H bond was not a factor in substrate affinity for the enzyme.     

Does Hydrogen Bonding Matter in Crystal Engineering? Crystal Structures of Salts of Isomeric Ions

The preparation and structure determinations of the crystalline salts [3,3'-H(2)bipy][PtCl(4)] (2), [2,2'-H(2)bipy][PtCl(4)] (3) and [1,4'-Hbipy][PtCl(4)] (4) and [3,3'-H(2)bipy][SbCl(5)] (6) and [1,4'-Hbipy][SbCl(5)] (8) are reported. In addition a redetermination of the structure of the metastable salt [4,4'-H(2)bipy][SbCl(5)] (5 b) in the corrected space group Pbcm is described. These structures are compared to those of the known salt [4,4'-H(2)bipy][PtCl(4)] (1), the stable triclinic form of [4,4'-H(2)bipy][SbCl(5)] (5 a) and [2,2'-H(2)bipy][SbCl(5)] (7). In the case of the salts of the rigid [PtCl(4)](2-) ion, structures 2, 3 and 4 are essentially isostructural despite the differing hydrogen-bonding capability of the cations. Similarly, among the salts of [SbCl(5)](2-) ions, structures 7 and 8 are essentially isostructural. Structure 6 differs from these in having a differing pattern of aggregation of the [SbCl(5)](2-) ions to form polymeric rather than tetrameric units. It is evident that local hydrogen-bonding interactions, although significant, are not the only or even the decisive influence on the crystal structures formed by these salts. These observations are not in good accord with the heuristic "sticky tecton" or supramolecular synthon models for synthetic crystallography or crystal engineering.     

To What Extent is FAIMS Beneficial in the Analysis of Proteins?

High field asymmetric waveform ion mobility spectrometry (FAIMS), also known as differential ion mobility spectrometry, is emerging as a tool for biomolecular analysis. In this article, the benefits and limitations of FAIMS for protein analysis are discussed. The principles and mechanisms of FAIMS separation of ions are described, and the differences between FAIMS and conventional ion mobility spectrometry are detailed. Protein analysis is considered from both the top-down (intact proteins) and the bottom-up (proteolytic peptides) perspective. The roles of FAIMS in the analysis of complex mixtures of multiple intact proteins and in the analysis of multiple conformers of a single protein are assessed. Similarly, the application of FAIMS in proteomics and targeted analysis of peptides are considered.

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Hydrogen Bonding and Aromatic π–π Stacking in the Crystal Structures of Water-Soluble Daidzein Derivatives

Water-soluble daidzein derivatives, [Ni(H₂O)₆](C₁₆H₁₁O₄SO₃)₂⋅10H₂O and [Zn(H₂O)₆] (C₁₆H₁₁O₄SO₃)₂⋅10H₂O (C₁₆H₁₁O₄SO₃, 7-methoxy-4′-hydroxylisoflavone-3′-sulfonate) were synthesized and their crystal structures were determined by X-ray diffraction analysis. The crystals of them all belong to triclinic crystal system, space group P . The results show that the two derivatives consist of metal cation [Ni(H₂O)₆]²⁺ and [Zn(H₂O)₆]²⁺, anion C₁₆H₁₁O₄SO₃⁻ and H₂O. Ni²⁺ and Zn²⁺ are the centers of the two compounds, respectively. A hydrophilic region is built by a variety of hydrogen bonds among [Ni(H₂O)₆]²⁺ or [Zn(H₂O)₆]²⁺, C₁₆H₁₁O₄SO₃⁻ and the lattice water molecules. Aromatic π–π stacking interactions assemble the isoflavone skeletons into a column and the columns form a hydrophobic region of daidzein derivatives. The sulfo-groups bridge the hydrophilic and hydrophobic region as well as the inorganic and organic components.     

Anion-π Interaction for Molecular Recognition of Anions: Focus on Cooperativity with Hydrogen Bonding

Anion recognition represents an active area of research in supramolecular chemistry. The last two decades have been marked by spectacular advances in the design of new anion receptors. Moreover, the development of approaches combining experimental and theoretical studies has proved to be particularly relevant, allowing for a better understanding and rationalization of the phenomena involved in anion complexation processes. In this context, the combination of weak interactions within the same receptor and their synergistic effects, called cooperativity, has attracted increasing interest within the scientific community. This Review focuses on the combination of anion-π and hydrogen bonds and the emerging concept of cooperativity. The most relevant anion-π donor families are presented. The concept of cooperativity is illustrated using the most recent examples present in current literature.     

Detection of Synthetic Antioxidants: What Factors Affect the Efficiency in the Chromatographic Analysis and in the Electrochemical Analysis?

Antioxidants are food additives largely employed to inhibit oxidative reactions in foodstuffs rich in oils and fat lipids, extending the shelf life of foodstuffs and inhibiting alterations in color, flavor, smell, and loss of nutritional value. However, various research has demonstrated that the inadequate use of synthetic antioxidants results in environmental and health problems due to the fact that some of these compounds present toxicity, and their presence in the human body, in high concentrations, is related to the development of some cancer types and other diseases. Therefore, the development of analytical methods for identifying and quantifying synthetic antioxidants in foodstuffs is fundamental to quality control and in ensuring consumer food safety. This review describes the recent chromatographic and electrochemical techniques used in the detection of synthetic phenolic antioxidants in foodstuffs, highlighting the main characteristics, advantages and disadvantages of these methods, and specific typical features, which include extraction methods for sample preparation and materials used in the working electrode construction, considering chromatographic and voltammetric methods, since these specific features influence the efficiency in the analysis.     

Prediction of the Physical Properties for the Ionic Liquid Based on Topological Index

1 INTRODUCTION As a new generation of solvent and catalyst, ionic liquid has captured intensive attention in the field of green chemistry[1, 2]. The most significant physical character is that its property can be changed with different choices of anions, cations and substituents. For example, the water solubility can be altered by choosing proper substituent on cation, and decreased by increasing the length of alkyl chain. On the other hand, critical change of its physical properties can …