Hydrogen bonding characterization of XH2NH2···HNO(X = B,Al, Ga) complexes: A theoretical investigation

The complexes of XH₂NH₂···HNO(X = B, Al, Ga) are characterized as head to tail with hydrogen bonding interactions. The structural characteristics can be confirmed by atoms in molecules (AIM) analysis, which also provide comparisons of hydrogen bonds strengths. The calculated interaction energies at G2MP2 level show that stability of complexes decrease as BH₂NH₂···HNO > AlH₂NH₂···HNO > GaH₂NH₂···HNO. On the basis of the vibrational frequencies calculations, there are red‐shifts for ν(X1? H) and blue‐shifts for ν(N? H) in the complexes on dihydrogen bonding formations (X1? H···H? N). On hydrogen bonding formations (N? H···O), there are red‐shifts for ν(N? H) compared to the monomers. Natural bond orbital (NBO) analysis is used to discuss the reasons for the ν(X1? H) and ν(N? H) stretching vibrational shifts by hyperconjugation, electron density redistribution, and rehybridization. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Intramolecular hydrogen bonding in 3‐imino‐propenylamine: Theoretical investigations

Intramolecular H‐bonds existing for derivatives of 3‐imino‐propenylamine have been studied using the B3LYP/6‐311++G** level of theory. The nature of these interactions, known as resonance‐assisted hydrogen bonds, has been discussed. Vibrational frequencies for α‐derivatives were calculated at the same level of theory. The topological properties of the electron density distributions for N? H···N intramolecular bridges have been analyzed in terms of the Bader theory of atoms in molecules (AIM). Calculation for 3‐imino‐propenylamine derivatives in water solution were also carried out at B3LYP/6‐311++G** level of theory. Finally, the analysis of hydrogen bond in this molecule and their derivatives by quantum theory of natural bond orbital methods fairly support the ab initio results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Interaction of the important species HNO and HFSO2 in the atmosphere: Theoretical study of the N?H and S?H blue‐shifted hydrogen bonds

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the N? H…O and S? H…O blue‐shifted H‐bonds in the HNO…HFSO₂ complex. The geometric structures, vibrational frequencies, and interaction energies were calculated by both standard and CP‐corrected methods. Natural bond orbital (NBO) analysis was used to investigate the origin of blue‐shifted H‐bonds, showing that the decrease in the σ*(N? H) and σ*(S? H) is due to the electron density redistribution effect. The structure reorganization effect on the blue‐shifted hydrogen bonds was discussed in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Optically active supramolecular complexes of water-soluble achiral polythiophenes and folic acid: spectroscopic studies and sensing applications

Optically active supramolecular complexes of water-soluble achiral polythiophene (PT) derivatives, PMTPA or PMTEA (Chart 1), and folic acid have been prepared; and the complex formation processes have been studied by absorption, emission, and circular dichroism (CD) spectroscopies. The complexes exhibited unique split-type induced CDs in the pi-pi* transition region of PTs, indicating that the molecular chirality of the glutamic acid moiety in folic acid was expressed in PT backbones. The influences of temperature, solvent composition, and the structures of the inducing molecules on the chirality induction to PTs were also investigated, and a possible mechanism for the formation of chiral superstructures was proposed. Furthermore, it was found that, upon addition of folic acid into aqueous solution of PTs (PMTPA or PMTEA), a dramatic color change from yellow to purple along with the emission quenching of PT derivatives was observed. PMTEA, having one fewer carbon in the hydrophobic side chain relative to PMTPA, showed better selectivity toward folic acid sensing over ATP because of its higher solubility in water and the appropriate hydrophilic/hydrophobic balance in the complex. Therefore, it can be applied as a colorimetric and fluorescent probe for detecting folic acid with high selectivity and sensitivity. Besides naked-eye detection of folic acid, the detection limit can be extended to be 10 (-8) M by using fluorometry and PMTEA as the probing molecule.     

Characterization of the N?H···ON and N?H···NO H‐bonds in nitrosamine dimers

Ab initio molecular orbital and DFT calculations have been carried out for three most stable dimers of parent nitrosamine (NA) in order to elucidate the structures and energetics of the dimers. The structures were optimized using HF, B3LYP, and MP2 methods with 6‐311+G(d,p) and 6‐311++G(2d,2p) basis sets. At the optimized geometries obtained at MP2/6‐311++G(2d,2p) level of theory, the energies were evaluated at QCISD/aug‐cc‐pVDZ and CCSD/aug‐cc‐pVDZ levels. The most stable dimer has two N? H···O?N hydrogen bonds and the least stable dimer has two N? H···N?O hydrogen bonds. The natural bond orbital analysis showed that the lpO(N) → BD*(N? N) and lpO(N) → BD*(N? H_b) interactions play a decisive role in the stabilization of the NH···O(N) hydrogen bonds in dimers. The atoms in molecules results reveal that the intermolecular N? H···O(N) H‐bonds in dimers have electrostatic character. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Ionic liquid based on α-amino acid anion and N7,N9-dimethylguaninium cation ([dMG][AA]): theoretical study on the structure and electronic properties

The interactions between five amino acid based anions ([AA](-) (AA = Gly, Phe, His, Try, and Tyr)) and N7,N9-dimethylguaninium cation ([dMG](+)) have been investigated by the hybrid density functional theory method B3LYP together with the basis set 6-311++G(d,p). The calculated interaction energy was found to decrease in magnitude with increasing side-chain length in the amino acid anion. The interaction between the [dMG](+) cation and [AA](-) anion in the most stable configurations of ion pairs is a hydrogen bonding interaction. These hydrogen bonds (H bonds) were analyzed by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Finally, several correlations between electron densities in bond critical points of hydrogen bonds and interaction energy as well as vibrational frequencies in the most stable configurations of ion pairs have been checked.     

Coupling properties of imidazole dimer radical cation assisted by embedded water molecule: toward understanding of interaction character of hydrogen-bonded histidine residue side-chains

Geometry optimizations are performed at the DFTB3LYP6-311+G* level. Four intriguing coupling modes, totally eight stable structures are found in the potential energy surfaces of the water-assisted coupling of imidazole dimer radical cation. In these isomers, the water molecules are embedded between two imidazole moieties, and the oxygen atom is tridentate or quadridentate, respectively. The distinct redshifts of the vibrational frequencies of the O-H...N and N-H...O type H bonds indicate the strong interaction of two imidazole rings of respective isomer. Inspection of the highest occupied molecular orbital predicts the alterations of the geometry structures on oxidation and reduction. The low barrier of the fragment rotation demonstrates that the isomerization processes by experiencing the distinct transition states are easy to fulfill, especially for those with O-H...N and C-H...O H bonds. Both the energy difference of the 0 degrees-cis and 180 degrees-trans orientation and the barriers of the fragment rotation are lowered by the water assisting. The range of the zero point vibrational energy correction indicates that the influence on the complexes with N-H...O and O-H...N H bonds (0.13-0.17 kcal/mol) is more significant than those with O-H...N and C-H...O H bonds (+/-0.03 kcal/mol). The dissociation energies of these isomers indicate that the charges transfer easily through water in the dissociation process and then are distributed mainly over the imidazole ring connecting with water molecule. The isomer with proton transfer between imidazole fragments is the most stable one.     

Theoretical study of the red‐ and blue‐shifted hydrogen bonds of nitroxyl and acetylene dimers

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the C? H…O red‐shifted and N? H…π blue‐shifted hydrogen bonds in HNO? C₂H₂ dimers. The geometric structures, vibrational frequencies and interaction energies were calculated by both standard and counterpoise (CP)‐corrected methods. In addition, the G3B3 method was employed to calculate the interaction energies. The topological and natural bond orbital (NBO) analysis were investigated the origin of N? H…π blue‐shifted hydrogen bond. From the NBO analysis, the electron density decrease in the σ* (N? H) is due to the significant electron density redistribution effect. The blue shifts of the N? H stretching frequency are attributed to a cooperative effect between the rehybridization and electron density redistribution. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Melaminium acetate acetic acid solvate monohydrate

The crystals of the title new melaminium salt, 2,4,6‐tri­amino‐1,3,5‐triazin‐1‐ium acetate acetic acid solvate monohydrate, C₃H₇N₆⁺·CH₃COO^?·CH₃COOH·H₂O, are built up from singly protonated melaminium residues, acetate anions, and acetic acid and water mol­ecules. The melaminium residues are interconnected by N—H?N hydrogen bonds to form chains along the [010] direction. These chains of melaminium residues form stacks aligned along the a axis. The acetic acid mol­ecules interact with the acetate anions via the H atom of their carboxylic acid groups and, together with the water mol­ecules, form layers that are parallel to the (001) plane. The oppositely charged moieties interact via multiple N—H?O hydrogen bonds that stabilize a pseudo‐two‐dimensional stacking structure.     

Intramolecular hydrogen bonding in derivatives of 3‐amino‐propenethial

Intramolecular H‐bonds existing for derivatives of 3‐amino‐propenethial have been studied using the B3LYP/6‐311++G** level of theory. The nature of these interactions, known as resonance assisted hydrogen bonds, has been discussed. The topological properties of the electron density distributions for N—H—S intramolecular bridges have been analyzed in terms of the Bader theory of atoms in molecules. Correlations between the H‐bond strength and topological parameters have been also studied. Furthermore, we obtained the exact value of the intramolecular hydrogen bond energies by the related rotamers method. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

A molecular orbital explanation for the B?N bond shortening in H3BNH3 on going from the gaseous to the solid state

A simple molecular orbital model has been applied to explanation of the B? N bond shortening in H₃BNH₃ on going from the gaseous to the solid state. In this model, the shortening is attributed to the bond order increase that is caused by the fact that each atom in the crystal experiences different external electrostatic potential to each other and thus the orbital energy level of each atom is changed. To illustrate this model, Effective Fragment Potential (EFP) method has been applied to the system consisting of a H₃BNH₃ molecule and 30 dipole moments whose magnitudes are determined by Lorentz's local field theory. This EFP computation has brought significant B? N bond shortening (1.668 → 1.623 Å), which is about 50% of the actual shortening. The factor of the remaining discrepancy has been analyzed by Morokuma decomposition under EFP and localized orbital analysis. These analyses have revealed that the remaining discrepancy is almost compensated by incorporating the dihydrogen bonds (B? H···H? N) that are formed by the orbital interaction between the bonding orbital of the B? H and the antibonding orbital of the N? H. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Reactivity of conjugated and unconjugated pterins with singlet oxygen (O2(1Deltag)): physical quenching and chemical reaction

Pterins (PTs) belong to a class of heterocyclic compounds present in a wide range of living systems. They participate in relevant biological functions and are involved in different photobiological processes. We have investigated the reactivity of conjugated PTs (folic acid [FA], 10-methylfolic acid [MFA], pteroic acid [PA]) and unconjugated PTs (PT, 6-hydroxymethylpterin [HPT], 6-methylpterin [MPT], 6,7-dimethylpterin [DPT], rhamnopterin [RPT]) with singlet oxygen (1O2) in aqueous solutions, and compared the efficiencies of chemical reaction and physical quenching. The chemical reactions between 1O2, produced by photosensitization, and PT derivatives were followed by UV-visible spectrophotometry and high-performance liquid chromatography, and corresponding rate constants (k(r)) were evaluated. Whenever possible, products were identified and quantified. Rate constants of 1O2 total quenching by the PT derivatives investigated were obtained from steady-state 1O2 luminescence measurements. Results show that the behavior of conjugated PTs differs considerably from that of unconjugated derivatives, and the mechanisms of 1O2 physical quenching by these compounds and of their chemical reaction with 1O2 are discussed in relation to their structural features.     

Elucidation of Metal‐Ion Accumulation Induced by Hydrogen Bonds on Protein Surfaces by Using Porous Lysozyme Crystals Containing RhIII Ions as the Model Surfaces

Metal‐ion accumulation on protein surfaces is a crucial step in the initiation of small‐metal clusters and the formation of inorganic materials in nature. This event is expected to control the nucleation, growth, and position of the materials. There remain many unknowns, as to how proteins affect the initial process at the atomic level, although multistep assembly processes of the materials formation by both native and model systems have been clarified at the macroscopic level. Herein the cooperative effects of amino acids and hydrogen bonds promoting metal accumulation reactions are clarified by using porous hen egg white lysozyme (HEWL) crystals containing Rh^III ions, as model protein surfaces for the reactions. The experimental results reveal noteworthy implications for initiation of metal accumulation, which involve highly cooperative dynamics of amino acids and hydrogen bonds: i) Disruption of hydrogen bonds can induce conformational changes of amino‐acid residues to capture Rh^III ions. ii) Water molecules pre‐organized by hydrogen bonds can stabilize Rh^III coordination as aqua ligands. iii) Water molecules participating in hydrogen bonds with amino‐acid residues can be replaced by Rh^III ions to form polynuclear structures with the residues. iv) Rh^III aqua complexes are retained on amino‐acid residues through stabilizing hydrogen bonds even at low pH (≈2). These metal–protein interactions including hydrogen bonds may promote native metal accumulation reactions and also may be useful in the preparation of new inorganic materials that incorporate proteins.     

Blue‐shifted and red‐shifted hydrogen bonds: Theoretical study of the CH3CHO· · ·HNO complexes

The blue‐shifted and red‐shifted H‐bonds have been studied in complexes CH₃CHO…HNO. At the MP2/6‐31G(d), MP2/6‐31+G(d,p) MP2/6‐311++G(d,p), B3LYP/6‐31G(d), B3LYP/6‐31+G(d,p) and B3LYP/6‐311++G(d,p) levels, the geometric structures and vibrational frequencies of complexes CH₃CHO…HNO are calculated by both standard and CP‐corrected methods, respectively. Complex A exhibits simultaneously red‐shifted C? H…O and blue‐shifted N? H…O H‐bonds. Complex B possesses simultaneously two blue‐shifted H‐bonds: C? H…O and N? H…O. From NBO analysis, it becomes evident that the red‐shifted C? H…O H‐bond can be explained on the basis of the two opposite effects: hyperconjugation and rehybridization. The blue‐shifted C? H…O H‐bond is a result of conjunct C? H bond strengthening effects of the hyperconjugation and the rehybridization due to existence of the significant electron density redistribution effect. For the blue‐shifted N? H…O H‐bonds, the hyperconjugation is inhibited due to existence of the electron density redistribution effect. The large blue shift of the N? H stretching frequency is observed because the rehybridization dominates the hyperconjugation. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

New insights in the atmospheric HONO formation: new pathways for N2O4 isomerization and NO2 dimerization in the presence of water

Isomerization of N(2)O(4) and dimerization of NO(2) in thin water films on surfaces are believed to be key steps in the hydrolysis of NO(2), which generates HONO, a significant precursor to the OH free radical in lower atmosphere and high-energy materials. Born-Oppenheimer molecular dynamics simulations using the density functional theory are carried out for NO(2)(H(2)O)(m), m ≤ 4, and N(2)O(4)(H(2)O)(n) clusters, n ≤ 7, used to mimic the surface reaction, to investigate the mechanism around room temperature. The results are (i) the NO(2) dimerization and N(2)O(4) isomerization reactions occur via two possible pathways, the non-water-assisted and water-assisted mechanisms; (ii) the NO(2) dimerization in the presence of water yields either ONONO(2)(H(2)O)(m) or NO(3)(-)NO(+)(H(2)O)(m) clusters, but it is also possible to form the HNO(3)(NO(2)(-))(H(3)O(+))(H(2)O)(m-2) transition state to form HONO and HNO(3), directly; (iii) the N(2)O(4) isomerization yields the NO(3)(-)NO(+)(H(2)O)(n) cluster, but it does not hydrolyze faster than the NO(2)(+)NO(2)(-)(H(2)O)(n) hydrolysis to directly form the HONO and HNO(3). New insights for hydrolysis of oxides of nitrogen in and on thin water films on surfaces in the atmosphere are discussed.     

Photochemical processes induced by vibrational overtone excitations: dynamics simulations for cis-HONO, trans-HONO, HNO3, and HNO3-H2O

Photochemical processes in HNO3, HNO3-H2O, and cis- and trans-HONO following overtone excitation of the OH stretching mode are studied by classical trajectory simulations. Initial conditions for the trajectories are sampled according to the initially prepared vibrational wave function. Semiempirical potential energy surfaces are used in "on-the-fly" simulations. Several tests indicate at least semiquantitative validity of the potential surfaces employed. A number of interesting new processes and intermediate species are found. The main results include the following: (1) In excitation of HNO3 to the fifth and sixth OH-stretch overtone, hopping of the H atom between the oxygen atoms is found to take place in nearly all trajectories, and can persist for many picoseconds. H-atom hopping events have a higher yield and a faster time scale than the photodissociation of HNO3 into OH and NO2. (2) A fraction of the trajectories for HNO3 show isomerization into HOONO, which in a few cases dissociates into HOO and NO. (3) For high overtone excitation of HONO, isomerization into the weakly bound species HOON is seen in all trajectories, in part of the events as an intermediate step on the way to dissociation into OH + NO. This process has not been reported previously. Well-established processes for HONO, including cis-trans isomerization and H hopping are also observed. (4) Only low overtone levels of HNO3-H2O have sufficiently long liftimes to be spectrocopically relevant. Excitation of these OH stretching overtones is found to result in the dissociation of the cluster H hopping, or dissociation of HNO3 does not take place. The results demonstrate the richness of processes induced by overtone excitation of HNO(x) species, with evidence for new phenomena. Possible relevance of the results to atmospheric processes is discussed.     

Silver(I)‐Catalyzed Tandem 1,3‐Acyloxy Migration/Mannich‐type Addition/Elimination of the Sulfonyl Group of N‐Sulfonylhydrazone‐propargylic Esters to 5,6‐Dihydropyridazin‐4‐one Derivatives

The addition of nucleophiles to C?N bonds offers a highly efficient synthetic strategy for accessing nitrogen‐containing molecules. 1 Among the well‐developed addition reactions, such as the highly efficient Mannich reaction, various C? H bond‐activated compounds including carboxylic acid derivatives, nitroalkanes, and terminal alkynes have been applied as nucleophiles to achieve different classes of amines. 2 However, employing new nucleophiles without activated C? H bonds, such as internal alkynes and allenic esters are limited when using metal catalysts. 3 Herein, we wish to report a new addition of allenic esters to C?N bonds initiated by a silver‐catalyzed 1,3‐migration of propargylic esters.     

Density functional theory study on hydrogen‐bonded complexes of adenine with polyformamide molecules

The structures of hydrogen‐bonded complexes A–F_n (n = 2–7) of adenine with polyformamide molecules have been fully optimized at B3LYP/6‐31G(d) basis set level. All the formamide molecules prefer to be N? H proton donor rather than C? H proton donor and are favorably bound to the five‐numbered moiety of adenine. A displacement of formamide molecules to one side of adenine mean plane has happened with an increasing number of formamide molecules. An obvious effect of hydrogen‐bonding cooperativity can be seen during the complex process. The most interesting geometrical change of adenine upon the complex is the shortening of the bond C4? N6 resulting from the strengthening of the conjugation between the π system of the adenine ring and the lone pair of the nitrogen atom. An existence of weak N? H···π bonding interaction between the π system of adenine and N? H bond of F7 is found and further conformed by an natural bond orbital analysis specially carried out on A–F₇. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Properties of strong hydrogen-bonded systems. II. Ab initioSCF-MO study of the hydrogen bond between nitric acid and ammonia

The hydrogen-bonded complex between nitric acid and ammonia molecules has been studied by the ab initio molecular orbital method using the 4-31G basis set. The calculated interaction energy for the complex (ΔE = ?91.4 kJ mole^?1) indicates that one is dealing with the strongest “nonionic” H-bonded complex considered hitherto by theoretical methods. Other properties of the hydrogen-bonded complex such as geometrical parameters, dipole moment, amount of charge transfer, and stretching force constants of the O? H and (OH)… N bonds are calculated and discussed.     

Theoretical studies on the influence of molecular interactions on the mechanism of electron transfer in photosynthetic reaction center of Rps.viridis

Based on the QM/MM optimized X-ray crystal structure of the photosynthetic reaction center (PRC) of purple bacteria Rhodopseudomonas (Rps.) viridis, quantum chemistry density functional method (DFT, B3LYP/6-31G) has been performed to study the interactions between the pigment molecules and either the surrounded amino acid residues or water molecules that are either axially coordinated or hydrogen bonded with the pigment molecules, leading to an explanation of the mechanism of the primary electron-transfer (ET) reactions in the PRC. Results show that the axial coordination of amino acid residues greatly raises the ELUMO of pigment molecules and it is important for the possibility of ET to take place. Different hydrogen bonds between amino acid residues, water molecules and pigment molecules decrease the ELUMO of the pigment molecules to different extents. It is crucial for the ET taking place from excited P along L branch and sustains that the ET is a one-step reaction without through accessory bacterioc