Theoretical calculation and vibrational spectral analysis of L-arginine trifluoroacetate

Fourier transform infrared and Raman spectra of the nonlinear optical crystal, L-arginine trifluoroacetate (L-arginine.CF3COOH, abbreviated as LATF) have been calculated by the first-principles calculation and investigated in experiment. The calculated results are slightly different from those experimental values because of the distinction resulted from the intermolecular hydrogen bonds. The role of this type of intermolecular interaction on the crystal vibrational spectra and nonlinear optical properties has been discussed. The absorption-edge on the IR side has been estimated by the theoretical approach on basis of the calculated infrared spectrum, which will be meaningful for further research on NLO crystal.     

Intermolecular interactions and dynamics of room temperature ionic liquids that have silyl- and siloxy-substituted imidazolium cations

The intermolecular interactions and dynamics of novel ionic liquids with alkylsilyl and alkylsiloxy substitutions on the cations are studied by measuring the intermolecular vibrational spectra and reorientational dynamics using femtosecond Kerr effect methods. The new ionic liquids include 1-dimethylphenylsilylmethyl-3-methylimidazolium (PhSi-mim+), and 1-methyl-3-pentamethyldisiloxymethylimidazolium (SiOSi-mim+) cations paired with the bis(trifluoromethylsulfonyl)imide (NTf(2)-) anion. Measured ionic liquid viscosities are surprisingly low for such bulky cation substituents. DFT electronic structure calculations on the isolated ions provide additional information about the electrostatic interactions.     

Intramolecular charge delocalization and nonlinear optical properties of push-pull chromophore 1-(4-N,N-dimethylaminopyridinium) acetic acid bromide monohydrate from vibrational spectra

FT-Raman and FT-IR spectra of the nonlinear optical crystal 1-(4-N,N-dimethylaminopyridinium) acetic acid bromide monohydrate have been recorded and analyzed. The equilibrium geometry, vibrational wavenumbers and the first order hyperpolarizability of the crystal have been calculated with the help of density functional theory computations. The assignments of the vibrational spectra have been carried out with the help of Scaled Quantum Mechanic force field theory. Optimized geometry gives the charge transfer interaction of the pyridine ring and the amino group in the electron-donor side of the nonlinear optic chromophore. Electron–phonon coupling and O–H?O interactions in making the molecule nonlinear optical active have been analyzed based on the vibrational spectral features. The Natural Bond Orbital analysis confirms the occurrence of strong intermolecular O–H?O hydrogen bonding.     

Influence of hydrogen bonds on charge distribution and conformation of L-arginine

The molecular recognition of adenosine-5'-triphosphate (ATP) with L-arginine (Arg) through hydrogen bonding interactions has been found using 1H NMR, H-H NOESY, acidity titration and fluorescence spectra techniques. The interactions could influence charge distribution in Arg and induce Arg conformational variation. It is realized that Arg conformation change from a partly folded state to an extended state through the rotation of CC single bonds of Arg side chain during the molecular recognition process.     

Structural criteria for the rational design of selective ligands: convergent hydrogen bonding sites for the nitrate anion

A large number of crystal structures are analyzed to characterize the structural aspects of hydrogen bonding interactions with the NO(3)(-) anion. Further insight is provided by the use of electronic structure calculations to determine stable geometries and interaction energies for NO(3)(-) complexes with several simple hydrogen bond donor groups, including water, methanol, N-methylform-amide, and methane. The results establish the existence of a clear set of structural criteria for the rational design of molecular receptors that complex the NO(3)(-) anion through hydrogen bonding interactions.     

方酸与2, 6-二苯并咪唑的超分子自组装及氢键实验与理论研究

在氘代的二甲基亚砜的溶剂中合成了方酸与2, 6-二苯并咪唑的超分子的化合物,并用X射线单晶衍射对其结构进行了表征。晶体结构分析表明:超分子是通过π-π堆积和分子之间氢键所形成的一维链状的聚合物。探讨了不同温度和不同浓度CCl₄溶剂对聚合物中氢键的影响。此外,用密度泛函理论和分子中原子理论对其进行了理论分析,计算结果表明分子间的键能分别是135.65和49.40 J·mol^-1。     

Pulsed ENDOR determination of the arginine location in the ferrous-NO form of neuronal NOS

Mammalian nitric oxide synthases (NOSs) are enzymes responsible for oxidation of L-arginine (L-Arg) to nitric oxide (NO). Mechanisms of reactions at the catalytic heme site are not well understood, and it is of current interest to study structures of the heme species that activates O(2) and transforms the substrate. The NOS ferrous-NO complex is a close mimic of the obligatory ferric (hydro)peroxo intermediate in NOS catalysis. In this work, pulsed electron-nuclear double resonance (ENDOR) was used to probe the position of the l-Arg substrate at the NO(?)-coordinated ferrous heme center(s) in the oxygenase domain of rat neuronal NOS (nNOS). The analysis of (2)H and (15)N ENDOR spectra of samples containing d(7)- or guanidino-(15)N(2) labeled L-Arg has resulted in distance estimates for the nearby guanidino nitrogen and the nearby proton (deuteron) at C(δ). The L-Arg position was found to be noticeably different from that in the X-ray crystal structure of nNOS ferrous-NO complex [Li et al. J. Biol. Inorg. Chem.2006, 11, 753-768], with the nearby guanidino nitrogen being ~0.5 ? closer to, and the nearby H(δ) about 1 ? further from, the NO ligand than in the X-ray structure. The difference might be related to the structural constraints imposed on the protein by the crystal. Importantly, in spite of its closer position, the guanidino nitrogen does not form a hydrogen bond with the NO ligand, as evidenced by the absence of significant isotropic hfi constant for N(g1). This is consistent with the previous reports that it is not the L-Arg substrate itself that would most likely serve as a direct proton donor to the diatomic ligands (NO and O(2)) bound to the heme.     

Three in One: The Versatility of Hydrogen Bonding Interaction in Halide Salts with Hydroxy-Functionalized Pyridinium Cations

The paradigm of supramolecular chemistry relies on the delicate balance of noncovalent forces. Here we present a systematic approach for controlling the structural versatility of halide salts by the nature of hydrogen bonding interactions. We synthesized halide salts with hydroxy-functionalized pyridinium cations [HOC_nPy]⁺ (n=2, 3, 4) and chloride, bromide and iodide anions, which are typically used as precursor material for synthesizing ionic liquids by anion metathesis reaction. The X-ray structures of these omnium halides show two types of hydrogen bonding: ‘intra-ionic’ H-bonds, wherein the anion interacts with the hydroxy group and the positively charged ring at the same cation, and ‘inter-ionic’ H-bonds, wherein the anion also interacts with the hydroxy group and the ring system but of different cations. We show that hydrogen bonding is controllable by the length of the hydroxyalkyl chain and the interaction strength of the anion. Some molten halide salts exhibit a third type of hydrogen bonding. IR spectra reveal elusive H-bonds between the OH groups of cations, showing interaction between ions of like charge. They are formed despite the repulsive interaction between the like-charged ions and compete with the favored cation-anion H-bonds. All types of H-bonding are analyzed by quantum chemical methods and the natural bond orbital approach, emphasizing the importance of charge transfer in these interactions. For simple omnium salts, we evidenced three distinct types of hydrogen bonds: Three in one!     

Spectroscopy study on the noncovalent interactions in the binary and ternary systems of L-lysine, adenosine 5'-triphosphate and magnesium ions

Intermolecular interactions of adenosine 5'-triphosphate (ATP) with Lysine (Lys) and Mg(2+) were studied in aqueous solution by (1)H and (31)P NMR spectra. In the metal-free system, the N-1 atom of the purine ring of ATP and carboxyl group of Lys are the interaction sites at low pH conditions. With increasing pH, the interaction efficiency between the phosphate group of ATP and the protonated ammonium group of Lys increased significantly, while that with carboxyl group in Lys decreased. In the Mg(2+)-Lys-ATP system, multi-interactions, such as coordination, cations (Mg(2+), NH(3)(+))-π, hydrogen bonding, ion-pairing interactions and electrostatic interactions co-existed. In addition, the recognition of ATP by the amino acid cation (Lys) was significantly promoted by the addition of magnesium ion, which led to the coordination competition between Lys and ATP.     

Electronic structural studies of pyrrolidinium-based ionic liquids for electrochemical application

Electrochemical stability and noncovalent interactions escorting the cyclic ammonium-based ionic liquids composed of N-alkyl-substituted N-methyl pyrrolidinium (P_yr1R) (R = methyl, ethyl, propyl, butyl, pentyl, hexyl) cations and four anions hexafluorophosphate (PF₆), tetrafluoroborate (BF₄), bis(trifluoromethylsulfonyl-imide (TFSI), and trifluoromethane sulfonate (TFO) have been analyzed using the density functional theory. Electronic structures, electrochemical window, frontier orbital energy difference (HOMO-LUMO gap), binding energies, vibrational spectra of these ion pairs were characterized. It has been established that ion pair formation is largely reigned by C H⋯F interactions between anionic fluorine for BF₄⁻ and PF₆⁻ anions and C H⋯O interactions between anionic oxygen for TFSI and TFO anions and pyrrolidinic proton, methyl, or alkyl group protons of the cations. The effect of alkyl chain length and pairing anions of the alkyl substituted N-methyl pyrrolidinium-based ionic liquids on the electrochemical window was investigated. The results revealed that the HOMO energy of pairing anions is the key factor to decide the electrochemical window. Further quantification of noncovalent interactions in terms of electrostatic and hydrogen bonding interactions has been brought out employing a novel method with the aid of Mulliken and Merz-Singh-Kollman charges, prevailed in pyrrolidinium-based ionic liquids.     

Vibrational analysis of 1-methyl-pyridinium-2-aldoxime and 1-methyl-pyridinium-4-aldoxime cations

Pyrimidinium aldoximes are administered intravenously in cases of acute organophosphate poisoning. Since questions regarding their morphology and active conformation in the solution are still open, an effort was made to establish correspondence between their crystal state conformers and vibrational spectra, thus facilitating the future work on the assignment of bands in solution. Normal coordinate analysis including the potential energy distribution for all modes was performed for 1-methyl-pyridinium-2-aldoxime (PAM2AN) and 1-methyl-pyridinium-4-aldoxime (PAM4AN) cations (charge=+e, spin=0). Positions of infrared and Raman bands of corresponding chloride salts agree rather well with predicted values, except for modes taking part in hydrogen bonding to anions. The strength of hydrogen bonding is estimated to be of medium strength in both salts, the bonding in PAM2AN being stronger. The calculated and observed values of the characteristic stretching modes for the aldoxime moiety have been in accordance with the stronger acidity of PAM2AN structural isomer.     

Reaction of perfluoro carbanions with mercury trifluoroacetate and trifluoromethylmercury trifluoroacetate

Conclusions The reaction of fluoroolefins and alkali metal fluorides with mercury trifluoroacetate and trifluoromethylmercury trifluoroacetate in polar aprotic solvents is a convenient method for the preparation of symmetrical and unsymmetrical bis(perfluoroalkyl)mercury compounds.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 7, pp. 1642–1643, July, 1974.     

Polarized vibrational studies of bisguanidinium hydrogenphosphate monohydrate

Detailed vibrational studies (FTIR and Raman on powder samples, polarized FTIR microscope on a small single crystal, polarized FTIR using Bruker reflection unit on a single crystal and polarized Raman) have been carried out. Vibrational spectra are discussed in relation to the crystal structure published previously. In this crystal a network of hydrogen bonds link water molecules, guanidinium cations and hydrogenphosphate ions. The 13 different hydrogen bonds in G2HP crystal structure are detected. On the basis of detailed vibrational studies the detailed assignment of observed bands was made. Calorimetric (DSC) studies have been performed, but no phase transition was found in the temperature range 100-350 K.     

Vibrational Dephasing in Ionic Liquids as a Signature of Hydrogen Bonding

Understanding both structure and dynamics is crucial for producing tailor‐made ionic liquids (ILs). We studied the vibrational and structural dynamics of medium versus weakly hydrogen‐bonded C?H groups of the imidazolium ring in ILs of the type [1‐alkyl‐3‐methylimidazolium][bis(trifluoromethanesulfonyl)imide] ([C_nmim][NTf₂]), with n=1, 2, and 8, by time‐resolved coherent anti‐Stokes Raman scattering (CARS) and quantum‐classical hybrid (QCH) simulations. From the time series of the CARS spectra, dephasing times were extracted by modeling the full nonlinear response. From the QCH calculations, pure dephasing times were obtained by analyzing the distribution of transition frequencies. Experiments and calculations reveal larger dephasing rates for the vibrational stretching modes of C(2)?H compared with the more weakly hydrogen‐bonded C(4,5)?H. This finding can be understood in terms of different H‐bonding motifs and the fast interconversion between them. Differences in population relaxation rates are attributed to Fermi resonance interactions.     

Application of CNDO/II to some hydrogen-bonded systems

Short results are given of the application of the CNDO/II method to hydrogen bonding. Formic acid (monomer and dimer), trifluoroacetic acid and the hydrogen bis(trifluoroacetate)ion were treated.     

Vibrational study of (CH3)4NSbCl6 and [(CH3)4N]2SiF6

(CH3)4NSbCl6 and [(CH3)4N]2SiF6 are face-centred cubic compounds at ambient temperature with a = 11.548 and 11.172 A, respectively. The vibrational spectra of these two compounds are discussed in relation to their crystal structure and other compounds containing (CH3)4N+ ions. The assignment of the observed bands is discussed. The Raman and infrared spectra of [(CH3)4N]2SiF6 show that the cations and anions are not distorted inside the crystals and are weakly hydrogen-bonded to each other. The infrared spectrum of (CH3)4NSbCl6 confirms a cubic structure for this compound at ambient temperature, in which cations are in octahedral environments and can be interpreted as being disordered groups. No evidence could be found for the existence of hydrogen bonding between cations and anions in this compound. The phase transition of (CH3)4NSbCI6 is studied by means of Raman spectroscopy. It is believed to be governed by the reorientational motions of tetramethylammonium cations and may be classified as an 'order-disorder' type.     

Hydrogen bonding and chemical shift assignments in carbazole functionalized isocyanides from solid-state NMR and first-principles calculations

Carbazole functionalized polyisocyanides are known to exhibit excellent electronic properties (E. Schwartz, et al., Chemistry of Materials, 2010, 22, 2597). The functionalities and properties of such materials crucially depend on the organization and stability of the polymer structure. We combine solid-state Nuclear Magnetic Resonance (NMR) experiments with first-principles calculations of isotropic chemical shifts, within the recently developed converse approach, to rationalize the origin of isotropic chemical shifts in the crystalline monomer l-isocyanoalanine 2-(9H-carbazol-9-yl) ethyl amide (monomer 1) and thereby gain insight into the structural organization of its polymer (polymer 2). The use of state-of-the-art solid-state NMR experiments combined with Density Functional Theory (DFT) based calculations allows an unambiguous assignment of all proton and carbon resonances of the monomer. We were able to identify the structure stabilising interactions in the crystal and understand the influence of the molecular packing in the crystal structure on the chemical shift data observed in the NMR spectra. Here the Nuclear Independent Chemical Shift (NICS) approach allows discriminating between 'physical' interactions amongst neighboring molecules such as ring-current effects and 'chemical' interactions such as hydrogen bonding. This analysis reveals that the isocyanide monomer is stabilized by multiple hydrogen bonds such as a bifurcated hydrogen bond involving -N-H, -C-H and O=C- moieties and Ar-H···C≡N- hydrogen bonding (Ar = aromatic group). Based on the geometrical arrangement it is postulated that the carbazole units are involved in the weak σ-π interactions giving rise to a Herringbone packing of the molecules. The chemical shift analysis of the polymer spectra readily establishes the existence of N-H···O=C hydrogen bonds despite the limited resolution exhibited by the polymer spectra. It is also elucidated that the relative arrangement of the carbazole units in the polymer differs significantly from that of the monomer.     

O-H stretch in phenol and its hydrogen-bonded complexes: band position and relaxation pathways

Anharmonic force fields are a suitable means for identification of vibrational degrees of freedom responsible for the peculiar shape of molecular spectra and the existence of diverse relaxation pathways. In this contribution, we investigated interactions that govern the position of the O-H stretching band in phenol and its dimers with water and ammonia. Dominant couplings are identified, and the nature of relaxation channels is analyzed. The effect of hydrogen bonding on O-H stretching motion and vibrational energy redistribution time through intra- and intermolecular interactions is studied, and possible vibrational predissociation upon O-H stretch excitation is addressed. The results based on computed anharmonic force constants are in accord with the available experimental findings.     

Bifurcated hydrogen bond in lithium nitrate trihydrate probed by ab initio molecular dynamics

The hydrogen-bond dynamics of lithium nitrate trihydrate has been studied by a combined approach based on ab initio molecular dynamics simulations and wavelet analysis. The simultaneous bifurcated interaction between one hydrogen atom of water molecules and two oxygen atoms of nitrate ions is the pivotal feature of the crystal structure: this bifurcated interaction has deep effects on the O-H stretching region of the vibrational spectrum. The structural, dynamic, spectroscopic, and electronic properties of the bifurcated hydrogen bond have been investigated computationally, elucidating at the molecular level the differences with weak and strong hydrogen bonds present in the crystal. These studies corroborate the very recent IR experiments performed on the lithium nitrate trihydrate crystal, offering new perspectives to interpreting the vibrational spectra. In fact, this approach allows obtaining two-dimensional plots, which summarize the essential features of both the hydrogen-bond network and IR spectra, resulting in a peculiar "signature" of the bifurcated interaction.     

Blue or green glowing crystals of the cation [Au{C(NHMe)2}2]+. Structural effects of anions, hydrogen bonding, and solvate molecules on the luminescence of a two-coordinate gold(I) carbene complex

Depending upon the crystallization conditions, [Au{C(NHMe) 2} 2](AsF 6) forms colorless crystals that display a blue or green luminescence. The difference involves the type of solvate molecule that is incorporated into the crystal and the structure of the chains of cations that are formed upon crystallization. The crystallographically determined structures of blue-glowing [Au{C(NHMe) 2} 2](AsF 6).0.5(benzene), blue-glowing [Au{C(NHMe) 2} 2](AsF 6).0.5(acetone), green-glowing [Au{C(NHMe) 2} 2](AsF 6).0.5(chlorobenzene), and blue-glowing, solvate-free [Au{C(NHMe) 2} 2](EF 6), E = P, As, Sb are reported. All pack with the cations forming extended columns, which may be linear or bent, but all show significant aurophilic interactions. The blue-glowing crystals have ordered stacks of cations with some variation in structural arrangement whereas the green-glowing crystals have disorder in their stacking pattern. Although there is extensive hydrogen bonding between the cations and anions in all structures, in the solvated crystals, the solvate molecules occupy channels but make no hydrogen-bonded contacts. The emission spectra of these new salts taken at 298 and 77 K are reported.