Gas‐phase intramolecular hydroxyl‐amino exchange of protonated arginine and verified by the synthetic intermediate compound

A new fragmentation process was proposed to interpret the characteristic product ion at m/z 130 of protonated arginine. The α‐amino group was dissociated from protonated arginine and then combined with the (M + H‐NH₃) fragment to form an ion‐neutral complex which further generated a hydroxyl‐amino exchange intermediate compound through an ion‐molecule reaction. This intermediate compound was synthesized from argininamide through a diazo reaction, and then the reaction mixture was analyzed using liquid chromatography combined with mass spectrometry (LC‐MS). The collision‐induced dissociation experiments under the same conditions revealed that this intermediate compound produced the characteristic product ion at m/z 130 as well as protonated arginine, and in addition, density functional theory calculations were performed to confirm simultaneous loss of NH₃ and CO from this intermediate to give the m/z 130 ion.     

A high-pressure mass spectrometric and density functional theory investigation of the thermochemical properties and structure of protonated dimers and trimers of glycine

A new modification of pulsed-ionization high-pressure mass spectrometry (PHPMS) has been used to perform equilibrium thermochemical studies for relatively nonvolatile biomolecules such as amino acids. Binding enthalpy and entropy changes have been measured for proton-bound clusters of glycine, which are in good agreement with both theoretical (DFT) results of this work and a previous blackbody infrared dissociation experiment. Experimental data indicate that a number of conformers of the proton-bound dimer of glycine may coexist in the explored temperature range (360-460 K). Several new, conceptually different isomers (two of them zwitterionic) have been found by DFT calculations, one of which is 7 kJ mol(-1) lower in energy than the structure previously reported to be the energy minimum.     

Gold-catalyzed intramolecular hydroarylation of olefins. Scope evaluation and preliminary mechanistic studies

We report a gold-catalyzed intramolecular hydroarylation of unactivated olefins using a combination of AuCl₃/AgOTf as the catalytic system affording dihydrobenzopyrans, tetralins and tetrahydroquinolines in good yields. For our preliminary mechanistic studies, we have investigated the kinetic isotope effects with deuterated arene compounds and found that this catalytic hydroarylation is consistent with an electrophilic aromatic substitution process.     

The effect of restricted intramolecular energy flow on the rate of one-substrate enzyme catalyzed reaction

We assume that the free intramolecular energy flow (intramolecular vibrational energy redistribution—IVR) between bonded substrate and enzyme can be restricted due to the presence of a metal atom near the binding site of enzyme. This restriction can represent one of the factors of enzyme catalysis. The concentration of energy evolved during the formation of enzyme-substrate complex in the bonded substrate enhances the reaction rate by several orders of magnitude in comparison with the case of free dissipation of evolved energy into the enzyme.     

The structure of protonated diamines and polyamines

The reduced mobilities in air, at 200C, of six isomeric C₇H₁₈N₂ protonated diamines, two triamines (caldine and spermidine), and two tetramines (thermine and spermine) were measured by ion mobility spectrometric (IMS) techniques. The results indicated that all these polyamines undergo proton-induced cyclization, with the proton forming a bridge between two amino groups. It appears as if the favored configuration of the protonated polyamines involves a six- or seven-membered ring rather than a bridge between the terminal amino groups. It is believed that in the tetramines the cyclic structure is formed between the two central, more basic, secondary amine sites.     

NMR and FTIR studies of coordinate-bonding and intramolecular and intermolecular hydrogen bonding in zinc(II)(3,5-diisopropylsalicylate)2

Carboxylate and salicylic OH coordinate bonding as well as intramolecular and intermolecular hydrogen bonding of bis-3,5-diisopropylsalicylatozinc(II), [Zn^II(3,5-DIPS)₂], with Lewis bases were studied to determine mechanisms accounting for antioxidant reactivity of Zn^II(3,5-DIPS)₂. Apparent thermodynamic parameters: K _eq, ΔS ⁰, ΔH ⁰, and ΔG ⁰ were determined for these equilibria with bonding of two molecules of dimethyl sulfoxide-d₆ (DMSO) or ethyl acetate-d₈ (EA) to the Zn^II using NMR and FTIR. We conclude that addition of two equivalents of DMSO or EA to non-polar solutions of Zn^II(3,5-DIPS)₂ results in bonding of DMSO or EA to Zn^II via sulfoxide or ester carbonyl oxygen atoms with ternary complex formation, leading to weakening of carboxylate and salicylic OH coordinate bonding to Zn^II and strengthening intramolecular hydrogen bonding between protons of salicylic OH groups and carboxylate oxygens. Subsequent addition of two or three additional equivalents of DMSO or EA leads to intermolecular hydrogen bonding between protons of salicylic OH groups.     

The effect of water‐mediated catalysis on the intramolecular proton‐transfer reactions of the isomers of 5‐chlorouracil: a theoretical study

The geometrical structures and thermal energies (E), enthalpies (H) and Gibbs free energies (G) of 13 isomers of 5‐chlorouracil (5ClU) in the gas and water phases were investigated using the density functional theory (DFT) method at the M06‐2X/6‐311++g(3df,3pd) level. The isomers of 5ClU can be microhydrated at different molecular target sites. The mono‐ and dihydrated forms are the most stable in both the gas and water phases, and, because of the intermolecular interactions, the hydrations lead to a degree of change in the stability trend. Two types of isomerizations were considered: the internal H—O bond rotations in which the H atom rotates 180° around the C—O bond and the intramolecular proton‐transfer reactions in which an H atom is transferred between an O atom and a neighbouring N atom. The forward and backward energy barriers for isomerizations of nonhydrated 5ClU were calculated. In addition, 16 optimized transition‐state structures for water‐mediated catalysis on isomerizations of 5ClU were investigated. The forward and backward proton‐transfer energy barriers of water‐mediated catalysis on isomerizations of 5ClU were obtained. The results indicate that the catalytic effect of two H₂O molecules is much greater than that of one H₂O molecule in isomerizations of 5ClU.     

IRMPD and ECD fragmentation of intermolecular cross-linked peptides

Despite the increasing number of studies using mass spectrometry for three dimensional analyses of proteins (MS3D), the identification of cross-linked peptides remains a bottleneck of the method. One of the main reasons for this is the lack of knowledge about the fragmentation of these species. Intermolecular cross-linked peptides are considered the most informative species present in MS3D experiment, since different peptides are connected by a cross-linker, the peptides chain can be either from a single protein, providing information about protein folding, or from two different proteins in a complex, providing information about binding partners, complex topology and interaction sites. These species tend to be large and highly charged in ESI, making comprehensive fragmentation by CID MS/MS problematic. On the other hand, these highly charged peptides are very suitable for dissociation using both infrared multiphoton dissociation (IRMPD) and electron capture dissociation (ECD). Herein, we report the fragmentation study of intermolecular cross-linked peptides using IRMPD and ECD. Using synthetic peptides and different commercial cross-linkers, a series of intermolecular cross-linked peptides were generate, and subsequently fragmented by IRMPD and ECD in a FT-ICR-MS instrument. Due to the high mass accuracy and resolution of the FT-ICR, the fragment ions could be attributed with high confidence. The peptides sequence coverage and fragmentation features obtained from IRMPD and ECD were compared for all charge states.     

Laser and synchrotron-based sources for excited state intramolecular dynamics studies

Energy ranges and time scales for excitation and relaxation of intramolecular processes are discussed and compared with the operational characteristics of laser and synchrotron radiation sources. The basic physics of synchrotron radiation and undulator emission is presented. It is shown how undulators can be used to generate short wavelength harmonics. Free electron lasers of the Compton and Raman scattering types and the associated electron beam sources are described. The properties and applications of free electron lasers are reviewed.     

Gas-phase nazarov cyclization of protonated 2-methoxy and 2-hydroxychalcone: An example of intramolecular proton-transport catalysis

Upon CA, ESI generated [M + H]⁺ ions of chalcone (benzalacetophenone) and 3-phenyl-indanone both undergo losses of H₂O, CO, and the elements of benzene. CA of the [M + H]⁺ ions of 2-methoxy and 2-hydroxychalcone, however, prompts instead a dominant loss of ketene. In addition, CA of the [M + H]⁺ ions of 2-methoxy-β-methylchalcone produces an analogous loss of methylketene instead. Furthermore, the [M + D]⁺ ion of 2-methoxychalcone upon CA eliminates only unlabeled ketene, and the resultant product, the [M + D − ketene]⁺ ion, yields only the benzyl-d ₁ cation upon CA. We propose that the 2-methoxy and 2-hydroxy (ortho) substituents facilitate a Nazarov cyclization to the corresponding protonated 3-aryl-indanones by mediating a critical proton transfer. The resultant protonated indanones then undergo a second proton transport catalysis facilitated by the same ortho substituents producing intermediates that eliminate ketene to yield 2-methoxy- or 2-hydroxyphenyl-phenyl-methylcarbocations, respectively. The basicity of the ortho substituent is important; for example, replacement of the ortho function with a chloro substituent does not provide an efficient catalyst for the proton transports. The Nazarov cyclization must compete with an alternate cyclization, driven by the protonated carbonyl group of the chalcone that results in losses of H₂O and CO. The assisted proton transfer mediated by the ortho substituent shifts the competition in favor of the Nazarov cyclization. The proposed mechanisms for cyclization and fragmentation are supported by high-mass resolving power data, tandem mass spectra, deuterium labeling, and molecular orbital calculations.     

Ab initio studies of three-membered ring formation through intramolecular nucleophilic substitution

Three-membered ring (3MR) forming processes of ⁻X(SINGLE BOND)CH₂(SINGLE BOND)CH₂(SINGLE BOND)F and ⁻CH₂(SINGLE BOND)C((SINGLE BOND)Y)(SINGLE BOND)CH₂(SINGLE BOND)F (X(DOUBLE BOND)CH₂, O, or S and Y(DOUBLE BOND)0 or S) through a gas phase neighboring group mechanism (S_Ni) are studied theoretically using the ab initio molecular orbital method with the 6–31+G* basis set. When electron correlation effects are considered, the activation (ΔG^≠) and reaction energies (ΔG⁰) are lowered by ca. 10 kcal mol⁻¹, indicating the importance of the electron correlation effect in these reactions. The contribution of entropy of activation (−TΔS^≠) at 298 K to ΔG^≠ is very small, and the reactions are enthalpy controlled. The ΔG^≠ and ΔG⁰ values for these ring closure processes largely depend on the stabilities of the reactants and the heteroatom acting as a nucleophilic center. The Bell–Evans–Polanyi principle applies well to all these reaction series. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1773–1784, 1997     

Chlorinated derivatives of c78-fullerene isomers with unusually short intermolecular halogen-halogen contacts

The chlorinated fullerenes C78(2)Cl18 and C78(3)Cl18 were synthesized by highly selective chlorination of the individual isomers. They were crystallized as C78(2)Cl18 x Br2 x TiCl4 and solvent free C78(3)Cl18. The carbon connectivities of both isomers have been confirmed through X-ray single-crystal analysis. Studious investigation of both crystal packings together with the crystal structure of C78(4)Cl18 has revealed the presence of unusually short intermolecular halogen-halogen contacts, which provide evidence for attractive intermolecular interactions, the nature of which is discussed.     

Blue shifts of the C-H stretching vibrations in hydrogen-bonded and protonated trimethylamine. Effect of hyperconjugation on bond properties

The optimized geometry of isolated trimethylamine (TMA), its hydrogen bond complexes with phenol derivatives and protonated TMA is calculated at the B3LYP/6-31++G(d,p) level. A natural bond orbital (NBO) analysis on these systems is carried out at the same level of theory. In isolated TMA, one of the C-H bond in each of the three CH(3) groups is more elongated than the two other ones. As revealed by the NBO data, this results from a hyperconjugative interaction from the N lone pair to the sigma*(C-H) orbitals of the C-H bonds being in a transoid position with respect to the N lone pair. The formation of an intermolecular OH...N hydrogen bond with phenols results in a decrease of the lone pair effect. A linear correlation is found between the decrease in occupation of the sigma*(C-H) orbitals and the decrease in the hyperconjugative interaction energy in the complexes and isolated TMA. Complex formation with phenols results in a blue shift of 55-74 cm(-1) of the C-H stretching vibrations involved in the lone pair effect. Smaller blue shifts between 14 and 23 cm(-1) are predicted for the other C-H bonds. In these complexes, a linear correlation is found between the frequency shifts and the elongation of the C-H bonds. Protonation of TMA results in a nearly equalization of all the C-H distances and a blue shift of 180 cm(-1) of the C-H bonds involved in hyperconjugation with the N lone pair.     

Polarons in one‐dimensional molecular chains with intermolecular and intramolecular vibrations

Polarons are investigated in a model for one‐dimensional molecular chains involving both acoustical and optical lattice vibrations, as found in diatomic chains. With the help of a specific ansatz for low‐lying quasiparticles, a continuum limit approximation sustains the existence of analytical solutions to the model. The dispersion energy as well as the effective mass of low‐lying electronic states in the presence of the two lattice mode‐induced polaronic quasiparticle, are derived analytically. It is found that the band effective mass is strongly enhanced by a factor depending on the two electron–lattice coupling constants. A test of stability of the analytical shapes of the three long‐wavelength excitations is carried out numerically by following their simultaneous propagation throughout the molecular lattice. The long‐wavelength polaron appears to be very stable within an acceptable range of values of the electron wave vector and propagates faster and faster as one moves from the groundstate toward mid‐band states. However, the accompanying kink and pulse soliton deformations are always slower consistently with the adiabatic considerations underlying the quasi‐classical treatment followed in this work. In addition, the kink component of the lattice deformation tends to become unstable at relatively large electronic wave vectors, while the polaron and in turn the optical lattice deformation are more and more stable, traducing dominant optical modes of the lattice in the process of formation of polaron. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Investigating the nature of intermolecular and intramolecular bonds in noble gas containing molecules

This article presents a theoretical study on a number of selected noble gas containing systems of the general formula FNgR and NgR (Ng = He, Ne, Ar, Kr, Xe and R = CH₃, CN, CCH, BO, BNH, H, BeO, and AuF). The principal structures, bond energies, spectroscopic, and electronic properties of 28 noble gas containing molecules were investigated using density functional theory at the BMK level. Quantum theory of atoms in molecules, natural bond orbital, and several other analysis methods have been used to provide more insight into the nature of noble gas bonds. Although both F? Ng and Ng? R bonds in the investigated molecules are assigned to have partially covalent and partially electrostatic nature, the covalent character is dominant in Ng? R bonds. In the second part, the intermolecular interactions between FNgR molecules and hydrogen fluoride are overviewed with emphasis on the hydrogen bonding through the fluorine side of noble gas molecule with hydrogen of HF. The calculated interaction energies were found to decrease in magnitude going down the noble gas series. For all noble gases, the strongest hydrogen bond has been observed in the case R=CH₃. On the contrary, using R=CN in the FNgR moiety weakens the interaction strength. © 2014 Wiley Periodicals, Inc.     

Theoretical studies of conjugation and substituent effect on intramolecular proton transfer in the ground and excited states

The ground- and excited-state intramolecular proton transfer (GSIPT and ESIPT) for 8-hydroxy-4H-naphthalen-1-one (HNA), 5-hydroxynaphthoquinone (HNQ), 1-hydroxy-anthraquione (HAQ), 7-hydroxy-1-indenone (7HIN), 5,8-dihydroxynaphthoquinone (DHNQ) and 4,9-dihydroxyperylene-3,10-quinone (DHP) are studied at B3LYP/6-31G(d,p) and TD B3LYP/6-31G(d,p) level. The calculated results show that the PES of GSIPT for HNA, HNQ and HAQ exhibit a single minimum in the enol zone, while for 7-HIN, DHNQ and DHP exhibit a double minimum and a high barrier between the two minima. The barrierless ESIPT for HNA is predicted, however, the PES of ESIPT for HNQ, HAQ, 7HIN, DHNQ and DHP exhibit a high barrier in the S₁ tautomerism.     

Adducts of acylphloroglucinols with explicit water molecules: Similarities and differences across a sufficiently representative number of structures

Acylphloroglucinols constitute a broad class of compounds, derivatives of 1,3,5‐trihydroxybenzene, characterized by at least one COR group and exhibiting a variety of biological activities. The presence of several hydrogen bond donor or acceptor sites (the three phenol OH of the phloroglucinol moiety and the sp² O of the COR group), and their comparatively close spacing, makes the study of adducts with explicit water molecules particularly interesting, because it is possible to consider adducts in which water molecules surround the entire acylphloroglucinol molecule, or a large part of it, providing expectedly realistic images of possible arrangements of water molecules in the close vicinity of the acylphloroglucinol molecule in the aqueous medium. This work considers a number of different monomeric structures sufficiently representative of the broad structural variety of acylphloroglucinols and considers adducts of all the relevant conformers for each structure. Calculations use the HF/6‐31G(d,p) level because of affordability reasons in view of the adducts' size. The results: show that the intramolecular hydrogen bond (IHB) between the sp² O of COR and an ortho OH does not break on competition with solute–solvent intermolecular H‐bonding; highlight general trends and trends related to specific geometry features of the conformers; enable an interpretation of the additional solvent stabilization of the conformers without IHBs, observed from polarizable continuum model results in water solution; and highlight the significance, for this class of compounds, of considering adducts in whichthe water molecules directly H‐bonded to the central molecule are bridged by other water molecules, to approximate a continuous layer. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2378–2390, 2010