Peptide cation-radicals. A computational study of the competition between peptide N-Calpha bond cleavage and loss of the side chain in the [GlyPhe-NH2 + 2H]+. cation-radical

Cation‐radicals and dications corresponding to hydrogen atom adducts to N‐terminus‐protonated N_α‐glycylphenylalanine amide (Gly‐Phe‐NH₂) are studied by combined density functional theory and Møller‐Plesset perturbational computations (B3‐MP2) as models for electron‐capture dissociation of peptide bonds and elimination of side‐chain groups in gas‐phase peptide ions. Several structures are identified as local energy minima including isomeric aminoketyl cation‐radicals, and hydrogen‐bonded ion‐radicals, and ylid‐cation‐radical complexes. The hydrogen‐bonded complexes are substantially more stable than the classical aminoketyl structures. Dissociations of the peptide N? C_α bonds in aminoketyl cation‐radicals are 18–47 kJ mol^?1 exothermic and require low activation energies to produce ion‐radical complexes as stable intermediates. Loss of the side‐chain benzyl group is calculated to be 44 kJ mol^?1 endothermic and requires 68 kJ mol^?1 activation energy. Rice‐Ramsperger‐Kassel‐Marcus (RRKM) and transition‐state theory (TST) calculations of unimolecular rate constants predict fast preferential N? C_α bond cleavage resulting in isomerization to ion‐molecule complexes, while dissociation of the C_α? CH₂C₆H₅ bond is much slower. Because of the very low activation energies, the peptide bond dissociations are predicted to be fast in peptide cation‐radicals that have thermal (298 K) energies and thus behave ergodically. Copyright © 2003 John Wiley & Sons, Ltd.     

The hydrochloride and hydrobromide salt forms of (S)‐amphetamine

Despite the high profile of amphetamine, there have been relatively few structural studies of its salt forms. The lack of any halide salt forms is surprising as the typical synthetic route for amphetamine initially produces the chloride salt. (S)‐Amphetamine hydrochloride [systematic name: (2S)‐1‐phenylpropan‐2‐aminium chloride], C₉H₁₄N⁺·Cl⁻, has a Z′ = 6 structure with six independent cation–anion pairs. That these are indeed crystallographically independent is supported by different packing orientations of the cations and by the observation of a wide range of cation conformations generated by rotation about the phenyl–CH₂ bond. The supramolecular contacts about the anions also differ, such that both a wide variation in the geometry of the three N—H...Cl hydrogen bonds formed by each chloride anion and differences in C—H...Cl contacts are apparent. (S)‐Amphetamine hydrobromide [systematic name: (2S)‐1‐phenylpropan‐2‐aminium bromide], C₉H₁₄N⁺·Br⁻, is broadly similar to the hydrochloride in terms of cation conformation, the existence of three N—H...X hydrogen‐bond contacts per anion and the overall two‐dimensional hydrogen‐bonded sheet motif. However, only the chloride structure features organic bilayers and Z′ > 1.     

Syntheses and Spectroscopic Study of Some New N‐4‐Fluorobenzoyl Phosphoric Triamides; Crystal Structures of 4‐F‐C6H4C(O)N(H)P(O)R2, R = NH‐C(CH3)3, NH‐CH2C6H5, N(CH3)(CH2C6H5)

Some new N‐4‐Fluorobenzoyl phosphoric triamides with formula 4‐F‐C₆H₄C(O)N(H)P(O)X₂, X = NH‐C(CH₃)₃ ( 1 ), NH‐CH₂‐CH=CH₂ ( 2 ), NH‐CH₂C₆H₅ ( 3 ), N(CH₃)(C₆H₅) ( 4 ), NH‐CH(CH₃)(C₆H₅) ( 5 ) were synthesized and characterized by ¹H, ¹³C, ³¹P NMR, IR and Mass spectroscopy and elemental analysis. The structures of compounds 1 , 3 and 4 were investigated by X‐ray crystallography. The P=O and C=O bonds in these compounds are anti. Compounds 1 and 3 form one dimensional polymeric chain produced by intra‐ and intermolecular ‐P=O···H‐N‐ hydrogen bonds. Compound 4 forms only a centrosymmetric dimer in the crystalline lattice via two equal ‐P=O···H‐N‐ hydrogen bonds. ¹H and ¹³C NMR spectra show two series of signals for the two amine groups in compound 1 . This is also observed for the two α‐methylbenzylamine groups in 5 due to the presence of chiral carbon atom in molecule. ¹³C NMR spectrum of compound 4 shows that ²J(P,C_aliphatic) coupling constant for CH₂ group is greater than for CH₃ in agreement with our previous study. Mass spectra of compounds 1 ‐ 3 (containing 4‐F‐C₆H₄C(O)N(H)P(O) moiety) indicate the fragments of amidophosphoric acid and 4‐F‐C₆H₄CN⁺ that formed in a pseudo McLafferty rearrangement pathway. Also, the fragments of aliphatic amines have high intensity in mass spectra.     

Di­methyl(2‐methyl­phenyl)­ammonium hydroxo­tris­(penta­fluoro­phenyl)­borate

In the title compound, [(CH₃)₂(C₇H₇)NH][(C₆F₅)₃B(OH)] or C₉H₁₄N⁺·C₁₈HBF₁₅O^?, the distorted tetrahedral borate anions are strongly hydrogen bonded to the substituted ammonium cations. The N?O separation in the N—H?O hydrogen bond is 2.728 (3) Å.     

Ethene elimination from CH3CH2NH=CH 2 + : Reaction pathways at the boundary between stepwise and concerted processes

The elimination of ethene from CH₃CH₂NH=CH ₂ ⁺ is characterized by ab initio procedures. This reaction occurs through several asynchronous stages, but without passing through formal intermediates. A potential energy barrier to hydrogen migration from the β carbon to N is largely determined by the energy required to cleave the CN bond, but is lowered slightly by H transfer from the β to the α carbon and then to N. The complex [C₂H ₅ ⁺ NH=CH₂] is bypassed, even though that complex could exist at energies only slightly above that of the transition state for ethene elimination. Furthermore, conversion of a substantial reverse activation energy into energy of motion causes CH₂=NH ₂ ⁺ and CH₂=CH₂ to dissociate faster than they can form [CH₂=NH ₂ ⁺ CH₂=CH₂]. Comparison of results for CH₃CH₂NH=CH ₂ ⁺ to ab initio ones for methane from CH₃CH₂CH ₃ ⁺ and elimination of ethene from CH₃CH₂O=CH ₂ ⁺ and CH₃CH₂CH=OH⁺ reveals that these dissociations occur in a similar but, in each case, a distinct series of asynchronous steps or stages, and that there is no sharp demarcation between concerted and stepwise eliminations as presently defined. In dissociations of CH₃CH₂NH=CH ₂ ⁺ , loss of electron density at the C in the breaking N bond leads the transfer of electron density to that carbon by migration of a hydrogen from the adjacent C. We attribute this to a requirement for the moving H to be close to Cα before the moving H can start to develop covalent bonding to Cα. It is also concluded that elimination of ethene from CH₃CH₂NH=CH ₂ ⁺ avoids a Woodward-Hoffmann symmetry-imposed barrier by H migrating sufficiently from the β to the α carbon on the way to N, so that the dissociation is essentially a 1,1 rather than a 1,2 elimination.     

On the effect of molecular structure on the superposition of normal modes of vibration

The normal modes of vibration in cartesian coordinates were calculated for ethylene, C₂H₄, and an ethylene complex, C₂H₄-Tl³⁺-H₂O, which is presumably formed during the catalytic oxidation of C₂H₄. For the CC bond of C₂H₄ as the critical coordinate of this reaction the distortions were then calculated which are caused by superimposing the normal modes. These calculations indicate that the maximum distortion of the CC bond which is attainable by superimposing normal modes in their ground state is larger in some conformations of the complex than in the free molecule. This indicates the general possibility that, depending on proper symmetry, complex formation may increase the reactivity of a compound because, compared to the free molecule, the superposition of a greater number of 3N-6 normal modes can produce greater momentary distortions of internal coordinates. The effect could be of considerable importance for the reactivity of very large systems, like, e.g., enzyme-substrate complexes.     

Surfing π Clouds for Noncovalent Interactions: Arenes versus Alkenes

A comparative study of molecular balances by NMR spectroscopy indicates that noncovalent functional‐group interactions with an arene dominate over those with an alkene, and that a π‐facial intramolecular hydrogen bond from a hydroxy group to an arene is favored by approximately 1.2 kJ mol^?1. The strongest interaction observed in this study was with the cyano group. Analysis of the series of groups CH₂CH₃, CH?CH₂, C?CH, and C?N shows a correlation between conformational free‐energy differences and the calculated charge on the C^α atom of these substituents, which is indicative of the electrostatic nature of their π interactions. Changes in the free‐energy differences of conformers show a linear dependence on the solvent hydrogen bond acceptor parameter β.     

Hexanamides intermédiaires de synthèse de pyridones-2 à partir de pyrones-2: étude physico-chimique (en particulier spectroscopique) des associations moléculaires

Methyl-6 hydroxy-4 pyridone-2 synthesis from methyl-6 hydroxy-4 pyrone-2 occurs through aliphatic intermediates RNHC (CH₃)CHCOCH₂CONHR (R=CH₃, C₆H₅, CH₂C₆H₅, CH₂CH₂C₆H₅). Dipole moments and spectroscopic measurements (especially IR spectroscopy) confirm that the tautomeric form observed in the solid state is also present in solution. This form is stabilized by intramolecular and intermolecular hydrogen bonds. Fundamental vibrations of hydrogen-bonded CO and NH (amido and amino) groups are assigned. The strength of hydrogen bond associations in various solvents is analysed with respect to the solid state.     

Infrared and Raman spectra and normal coordinate calculations for methylisothiocyanate

The infrared spectra (3200-50 cm^?1) of gaseous and solid CH₃NCS and CD₃NCS and the Raman spectra (3200-10 cm^?1) of the liquids and solids have been recorded. The spectra have been interpreted on the basis of a “pseudo-symmetric top” with C_3v symmetry. An assignment of the fundamental vibrations in both molecules, based on their infrared band contours, depolarization values and group frequencies, is given and discussed. Particularly interesting is the low-frequency region where band maxima were observed at 152 and 80 cm^?1 for CH₃NCS and 139 and 71 cm^?1 for CD₃NCS in the infrared spectra of the gases. A normal coordinate analysis has also been carried out based on C_3v symmetry. Considerable mixing was found between the C_αN stretch and NCS symmetric stretch in both isotopic species. The other normal modes in CH₃NCS are reasonably pure but, for the CD₃NCS molecule, considerable mixing was found between the CD₃ stretches and NCS antisymmetric stretch. The proposed vibrational assignment and the results of the normal coordinate calculations are discussed and compared with the results obtained for similar molecules.     

Nonadditivity of methyl group in single‐electron hydrogen bond of methyl radical‐water complex

The nonadditivity of methyl group in the single‐electron hydrogen bond of the methyl radical‐water complex has been studied with quantum chemical calculations at the UMP2/6‐311++G(2df,2p) level. The bond lengths and interaction energies have been calculated in the four complexes: CH₃? H₂O, CH₃CH₂? H₂O, (CH₃)₂CH? H₂O, and (CH₃)₃C? H₂O. With regard to the radicals, tert‐butyl radical forms the strongest hydrogen bond, followed by iso‐propyl radical and then ethyl radical; methyl radical forms the weakest hydrogen bond. These properties exhibit an indication of nonadditivity of the methyl group in the single‐electron hydrogen bond. The degree of nonadditivity of the methyl group is generally proportional to the number of methyl group in the radical. The shortening of the C···H distance and increase of the binding energy in the (CH₃)₂CH? H₂O and (CH₃)₃C? H₂O complexes are less two and three times as much as those in the CH₃CH₂? H₂O complex, respectively. The result suggests that the nonadditivity among methyl groups is negative. Natural bond orbital (NBO) and atom in molecules (AIM) analyses also support such conclusions. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Different hydrogen-bonding patterns in two [Zn(ENTPP)] complexes with water or methanol as ligands

We have synthesized zinc complexes of H₂ENTPP (5-(8-ethoxycarbonyl-1-naphthyl)-10,15,20-triphenyl porphyrin) as a model to study hydrogen-bonding interactions. When water or methanol is a ligand, crystals of [Zn(ENTPP)(CH₃OH)] or [Zn(ENTPP)(H₂O)]?·?C₆H₅CH₃ were obtained. In both structures, the ligand has hydrogen-bonding interactions, but in different patterns. In [Zn(ENTPP)(CH₃OH)], the methanol oxygen and carboxylate oxygen in the naphthyl group form an intermolecular hydrogen bond. In [Zn(ENTPP)(H₂O)]?·?C₆H₅CH₃, there are two independent molecules A and B. In molecule B, there is an intramolecular hydrogen bond between the water oxygen and the carboxylate oxygen, while in molecule A, besides the intramolecular hydrogen bond, there is an intermolecular hydrogen bond between the water oxygen and the carboxylate oxygen. ¹H NMR spectra suggest the binding of methanol or water to zinc are equilibrium processes in solution. Equilibrium constant has been determined by UV-Vis measurements, and it suggests the binding affinity of zinc to methanol has been moderately increased.     

Vibrational spectra and dynamics of conformation and hydrogen bonding of n-methylacetamide. I. Conformational dynamics of the CH3CONHCH3 molecule and NH out of plane band splitting

The infrared spectra of CH₃CONHCH₃ and CH₃CONDCH₃ have been investigated as low temperature crystals, pure liquids and solutions in various solvents in the 400-800 cm^?1 range. A new assignment of the bands associated with the NH group is given. Multiplets of γ NH and γ ND fundamentals have generally been observed and have been interpreted in terms of a double minimum potential function of the γ NH mode with a tunnelling between two minima. The potential functions of γ NH and τ CN modes are similar and can be combined to give a potential surface with four minima corresponding to four molecular conformations. The influence of the hydrogen bonding on the γ NH splitting and barrier height is discussed.     

Thermal Ethane Activation by Bare [V2O5]+ and [Nb2O5]+ Cluster Cations: on the Origin of Their Different Reactivities

The gas‐phase reactivity of [V₂O₅]⁺ and [Nb₂O₅]⁺ towards ethane has been investigated by means of mass spectrometry and density functional theory (DFT) calculations. The two metal oxides give rise to the formation of quite different reaction products; for example, the direct room‐temperature conversions C₂H₆→C₂H₅OH or C₂H₆→CH₃CHO are brought about solely by [V₂O₅]⁺. In distinct contrast, for the couple [Nb₂O₅]⁺/C₂H₆, one observes only single and double hydrogen‐atom abstraction from the hydrocarbon. DFT calculations reveal that different modes of attack in the initial phase of C?H bond activation together with quite different bond‐dissociation energies of the M?O bonds cause the rather varying reactivities of [V₂O₅]⁺ and [Nb₂O₅]⁺ towards ethane. The gas‐phase generation of acetaldehyde from ethane by bare [V₂O₅]⁺ may provide mechanistic insight in the related vanadium‐catalyzed large‐scale process.     

Thioacetanilide at 120 K

The title compound, C₈H₉NS, has four symmetry‐independent molecules in the asymmetric unit. These molecules link into two independent infinite N—H...S hydrogen‐bonded chains in the a‐axis direction with graph‐set notation C₂²(8). The NH—CS group adopts a trans conformation and forms a dihedral angle of about 50° with the phenyl ring. The intermolecular hydrogen‐bond energy calculated by the density functional theory (DFT) method is −14.95 kJ mol⁻¹. The correlation between the IR spectrum of this compound and the hydrogen‐bond energy is also discussed. This molecular system is of interest because of its biological function.     

Hydrogen bond effect on the bonding and B2 molecular vibrations of pyrrole

The influence of the hydrogen bond on the infrared B₂ symmetry modes of pyrrole (C_2ν) has been studied. CNDO/2 calculations suggest that the most probable structure for the associated pyrrole involves the interaction NH ⋯ π. The shortest distance between the nitrogen atom and the ring of the nearest neighbor molecule is about 2.9 Å. The absorption bands of pyrrole in the gaseous state at 474, 626 and 720 and 826 cm⁻¹ have been assigned to the NH, ring and CH out-of-plane deformation modes.     

Correlated one‐electron wave functions

Using four basis sets, 6‐311G(d,p), 6‐31+G(d,p), 6‐311++G(2d,2p), and 6‐311++G(3df,3pd), the optimized structures with all real frequencies were obtained at the MP2 level for dimers CH₂O? HF, CH₂O? H₂O, CH₂O? NH₃, and CH₂O? CH₄. The structures of CH₂O? HF, CH₂O? H₂O, and CH₂O? NH₃ are cycle‐shaped, which result from the larger bend of σ‐type hydrogen bonds. The bend of σ‐type H‐bond O…H? Y (Y?F, O, N) is illustrated and interpreted by an attractive interaction of a chemically intuitive π‐type hydrogen bond. The π‐type hydrogen bond is the interaction between one of the acidic H atoms of CH₂O and lone pair(s) on the F atom in HF, the O atom in H₂O, or the N atom in NH₃. By contrast with above the three dimers, for CH₂O? CH₄, because there is not a π‐type hydrogen‐bond to bend its linear hydrogen bond, the structure of CH₂O? CH₄ is a noncyclic shaped. The interaction energy of hydrogen bonds and the π‐type H‐bond are calculated and discussed at the CCSD(T)/6‐311++G(3df,3pd) level. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Interaction of the Benzenium Ion with Inert Ligands: IR Spectra of C6H7+?Ln Cluster Cations (L=Ar,N2, CH4, H2O)

IR photodissociation spectra of mass‐selected clusters composed of protonated benzene (C₆H₇⁺) and several ligands L are analyzed in the range of the C? H stretch fundamentals. The investigated systems include C₆H₇⁺? Ar, C₆H₇⁺? (N₂)_n (n=1–4), C₆H₇⁺? (CH₄)_n (n=1–4), and C₆H₇⁺? H₂O. The complexes are produced in a supersonic plasma expansion using chemical ionization. The IR spectra display absorptions near 2800 and 3100 cm^?1, which are attributed to the aliphatic and aromatic C? H stretch vibrations, respectively, of the benzenium ion, that is, the σ complex of C₆H₇⁺. The C₆H₇⁺? (CH₄)_n clusters show additional C? H stretch bands of the CH₄ ligands. Both the frequencies and the relative intensities of the C₆H₇⁺ absorptions are nearly independent of the choice and number of ligands, suggesting that the benzenium ion in the detected C₆H₇⁺? L_n clusters is only weakly perturbed by the microsolvation process. Analysis of photofragmentation branching ratios yield estimated ligand binding energies of the order of 800 and 950 cm^?1 (≈9.5 and 11.5 kJ mol^?1) for N₂ and CH₄, respectively. The interpretation of the experimental data is supported by ab initio calculations for C₆H₇⁺? Ar and C₆H₇⁺? N₂ at the MP 2/6‐311 G(2df,2pd) level. Both the calculations and the spectra are consistent with weak intermolecular π bonds of Ar and N₂ to the C₆H₇⁺ ring. The astrophysical implications of the deduced IR spectrum of C₆H₇⁺ are briefly discussed.     

The synergistic cooperation of NH⋯O and CH⋯O hydrogen bonds in the structures of three new phosphoric triamides

The supramolecular assemblies of three new phosphoric triamides, {(C₆H₅CH₂)(CH₃)N}₂(4-CH₃-C₆H₄C(O)NH)P(O) (1), {(C₆H₁₁)(CH₃)N}₂(4-CH₃-C₆H₄C(O)NH)P(O) (2) and {(C₂H₅)₂N}₂(4-CH₃-C₆H₄C(O)NH)P(O) (3) were studied by single crystal X-ray diffraction as well as by Hirshfeld surface analysis. It was found that a synergistic cooperation of NH?O and CH?O hydrogen bonds occurs in all three structures, but forming unique supramolecular architectures individually. Along with the presence of centrosymmetric dimers in 1, 2 and 3, based on a classical NH?O hydrogen bond, the presence of weak CH?O interactions play an additional and vital role in crystal architecture and construction of the final assemblies, collectively identified as a centrosymmetric dimer (0D), a 1-D array and a 3-D network, respectively. These differences in superstructures are related to the effect of aromatic, bulk and flexible groups used in the molecules designed, with a similar C(O)NHP(O) backbone. The NH?O contacts in 1, 2 and 3 are of the “resonance-assisted hydrogen bond” types and also the anti-cooperativity effect can be considered in the multi-acceptor sites P═O in 1 and 2 and C═O in 3. All three compounds were further studied by 1D NMR experiments, 2D NMR techniques (HMQC and HMBC (H–C correlation)), high resolution ESI–MS, EI–MS spectrometry and IR spectroscopy methods.     

Uncommon hydrogen bonds between a non-classical ethyl cation and π hydrocarbons: a preliminary study

This study undertakes a theoretical investigation into uncommon hydrogen bonds between the ethyl cation (C₂H₅ ⁺) and π hydrocarbons. Firstly, it considers the hyperconjugation effect of the ethyl cation, in which the non-localized hydrogen (H⁺) is taken to be a pseudoatom bound to the carbons of the methyl groups. The goal of the research is to use this electronic phenomenon to gain a better understanding of the (H⁺···π) and (H⁺···p-π) hydrogen bonds, which are considered uncommon because they are formed through the interaction of the H⁺ of the ethyl cation with the π bonds of the acetylene (C₂H₂) and ethene (C₂H₄), as well as with the pseudo-π bond of the cyclopropane (C₃H₆). In view of this, B3LYP/6-311++G(d,p) calculations were used to determine the geometries of the C₂H₅ ⁺···C₂H₂, C₂H₅ ⁺···C₂H₄, and C₂H₅ ⁺···C₃H₆ hydrogen-bonded complexes. Deformations of the bond lengths and bond angles of these systems were analyzed geometrically. Examination of the stretch frequencies and absorption intensities of the (H⁺···π) and (H⁺···p-π) hydrogen bonds has revealed red-shifts in π and p-π bonds. After structural modeling and vibrational characterization, analysis of the charge transfer following the ChelpG approach and subsequently quantification of the hydrogen bond energies (basis sets superpostition error and zero point vibrational energies being considered) were used to predict the strength of the (H⁺···π) and (H⁺···p-π) hydrogen bonds. In addition, the molecular topography was estimated using the quantum theory of atoms in molecules (QTAIM). QTAIM was chosen because of a desire to understand the (H⁺···π) and (H⁺···p-π) hydrogen bonds chemically on the basis of the quantity of charge density and interpretation of Laplacian fields. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Pseudopolymorphs of chelidamic acid and its dimethyl ester

Different tautomeric and zwitterionic forms of chelidamic acid (4‐hydroxypyridine‐2,6‐dicarboxylic acid) are present in the crystal structures of chelidamic acid methanol monosolvate, C₇H₅NO₅·CH₄O, (Ia), dimethylammonium chelidamate (dimethylammonium 6‐carboxy‐4‐hydroxypyridine‐2‐carboxylate), C₂H₈N⁺·C₇H₄NO₅⁻, (Ib), and chelidamic acid dimethyl sulfoxide monosolvate, C₇H₅NO₅·C₂H₆OS, (Ic). While the zwitterionic pyridinium carboxylate in (Ia) can be explained from the pK_a values, a (partially) deprotonated hydroxy group in the presence of a neutral carboxy group, as observed in (Ib) and (Ic), is unexpected. In (Ib), there are two formula units in the asymmetric unit with the chelidamic acid entities connected by a symmetric O—H...O hydrogen bond. Also, crystals of chelidamic acid dimethyl ester (dimethyl 4‐hydroxypyridine‐2,6‐dicarboxylate) were obtained as a monohydrate, C₉H₉NO₅·H₂O, (IIa), and as a solvent‐free modification, in which both ester molecules adopt the hydroxypyridine form. In (IIa), the solvent water molecule stabilizes the synperiplanar conformation of both carbonyl O atoms with respect to the pyridine N atom by two O—H...O hydrogen bonds, whereas an antiperiplanar arrangement is observed in the water‐free structure. A database study and ab initio energy calculations help to compare the stabilities of the various ester conformations.