Fragmentations of protonated arginine, lysine and their methylated derivatives: concomitant losses of carbon monoxide or carbon dioxide and an amine

The fragmentation pathways of protonated arginine, protonated N(alpha),N(alpha)-dimethylarginine, the N(alpha),N(alpha),N(alpha)-trimethylarginine ion, three protonated N(epsilon),N(epsilon)-dimethyllysines, and three permanent lysine ions in which the charge is fixed by trimethylation are reported. Ion assignment was facilitated by (15)N-labeling and deuterium substitution. The chemistries are dominated by charge-induced elimination of the amino groups as neutrals, including dimethylamine, trimethylamine and guanidine. Competitive losses of the alpha-amino and side-chain amino groups were observed; these losses led to intermediates that had different structures and different subsequent dissociation reactions. Concomitant losses of CO or CO(2) with these amines were also commonly observed. However, the ionic products of amine losses did not subsequently lose CO or CO(2), suggesting strongly that in these concomitant eliminations, it is the CO or CO(2) that was first eliminated, followed immediately by the loss of the amine. Results of density functional theory calculations on protonated arginine and protonated N(alpha),N(alpha)-dimethylarginine reveal that, in such concomitant eliminations, the dissociating complex is vibrationally hot and the intermediate ion formed by losing CO or CO(2) can immediately dissociate to eliminate the amine.     

Binding energies of protonated betaine complexes: a probe of zwitterion structure in the gas phase

The dissociation kinetics of proton-bound dimers of betaine with molecules of comparable gas-phase basicity were investigated using blackbody infrared radiative dissociation (BIRD). Threshold dissociation energies were obtained from these data using master equation modeling. For bases that have comparable or higher gas-phase basicity, the binding energy of the protonated base.betaine complex is ~1.4 eV. For molecules that are ~2 kcal/mol or more less basic, the dissociation energy of the complexes is ~1.2 eV. The higher binding energy of the former is attributed to an ion-zwitterion structure which has a much larger ion-dipole interaction. The lower binding energy for molecules that are ~2 kcal/mol or more less basic indicates that an ion-molecule structure is more favored. Semiempirical calculations at both the AM1 and PM3 levels indicate the most stable ion-molecule structure is one in which the base interacts with the charged quaternary ammonium end of betaine. These results indicate that the measurement of binding energies of neutral molecules to biological ions could provide a useful probe for the presence of zwitterions and salt bridges in the gas phase. From the BIRD data, the gas-phase basicity of betaine obtained from the kinetic method is found to be 239.2 +/- 1.0 kcal/mol. This value is in excellent agreement with the value of 239.3 kcal/mol (298 K) from ab initio calculations at the MP2/6-31+g** level. The measured value is slightly higher than those reported previously. This difference is attributed to entropy effects. The lower ion internal energy and longer time frame of BIRD experiments should provide values closer to those at standard temperature.     

Proton migration and tautomerism in protonated triglycine.

Proton migration in protonated glycylglycylglycine (GGG) has been investigated by using density functional theory at the B3LYP/6-31++G(d,p) level of theory. On the protonated GGG energy hypersurface 19 critical points have been characterized, 11 as minima and 8 as first-order saddle points. Transition state structures for interconversion between eight of these minima are reported, starting from a structure in which there is protonation at the amino nitrogen of the N-terminal glycyl residue following the migration of the proton until there is fragmentation into protonated 2-aminomethyl-5-oxazolone (the b(2) ion) and glycine. Individual free energy barriers are small, ranging from 4.3 to 18.1 kcal mol(-)(1). The most favorable site of protonation on GGG is the carbonyl oxygen of the N-terminal residue. This isomer is stabilized by a hydrogen bond of the type O-H.N with the N-terminal nitrogen atom, resulting in a compact five-membered ring. Another oxygen-protonated isomer with hydrogen bonding of the type O-H.O, resulting in a seven-membered ring, is only 0.1 kcal mol(-)(1) higher in free energy. Protonation on the N-terminal nitrogen atom produces an isomer that is about 1 kcal mol(-)(1) higher in free energy than isomers resulting from protonation on the carbonyl oxygen of the N-terminal residue. The calculated energy barrier to generate the b(2) ion from protonated GGG is 32.5 kcal mol(-)(1) via TS(6-->7). The calculated basicity and proton affinity of GGG from our results are 216.3 and 223.8 kcal mol(-)(1), respectively. These values are 3-4 kcal mol(-)(1) lower than those from previous calculations and are in excellent agreement with recently revised experimental values.     

Excited state tautomerization of azaindole

Fluorescent tryptophan analogs, like azatryptophan, offer an advantage for exploring protein and peptide structure and dynamics. The chromophoric moieties, azaindole, of the azatryptophan analogs are investigated for their potential as fluorescent probes. The photophysical properties of 4-azaindole (4AI) and 5-azaindole (5AI) and their tautomers are characterized through computational and experimental methods. Both 4AI and 5AI undergo excited state tautomerization in the presence of 1 M NaOH. The protonated forms of 4AI and 5AI have a fluorescence emission of 415 and 410 nm, respectively, while the tautomers of 4AI and 5AI have a fluorescent emission of 480 and 450 nm, respectively. Gas phase computations (B3LYP/6-31+G**) show that the N1H azaindole tautomer is lower in energy in the ground state by as much as 12.5 kcal mol(-1), while the N(n)H azaindole tautomer is lower in energy in the excited state by as much as 18.1 kcal mol(-1). Solvent effects on the tautomer energy differences were computed using the isodensity polarized continuum model (IPCM). The polarity of the solvent helps to reduce the energy difference between the tautomers in the ground state by as much as 5.8 kcal mol(-1), but not enough to reverse the ground state tautomer preference.     

Elimination of water from the carboxyl group of GlyGlyH+

The elimination of water from the carboxyl group of protonated diglycine has been investigated by density functional theory calculations. The resulting structure is identical to the b(2) ion formed in the mass spectrometric fragmentation of protonated peptides (therefore named "b2" in this study). The most stable geometry of the fragment ion ("b2") is an O-protonated diketopiperazine. However, its formation is kinetically disfavored as it requires a free energy of 58.2 kcal/mol. The experimentally observed N-protonated oxazolone is 3.0 kcal/mol less stable. The lowest energy pathway for the formation of the "b2" ion requires a free energy of 37.5 kcal/mol and involves the proton transfer from the amide oxygen of protonated diglycine to the hydroxyl oxygen. Fragmentation initiated by proton transfer from the terminal nitrogen has also a comparable free energy of activation (39.4 kcal/mol). Proton transfer initiating the fragmentation, from the highly basic terminal nitrogen or amide oxygen to the less basic hydroxyl oxygen is feasible at energies reached in usual mass spectrometric experiments. Amide N-protonated diglycine structures are precursors of mainly y(1) ions rather than "b2" ions. In the lowest energy fragmentation channels, proton transfer to the hydroxylic oxygen, bond breaking and formation of an oxazolone ring occur concertedly but asynchronously. Proton transfer to hydroxyl oxygen and cleavage of the corresponding C-O bond take place at the early stages of the fragmentation step, while ring closure to form an oxazolone geometry occurs at the later stages of the transition. The experimentally observed low kinetic energy release is expected to be due to the existence of a strongly hydrogen bonded protonated oxazolone-water complex in the exit channel. Whereas the threshold energy for "b2" ion formation (37.1 kcal/mol) is lower than for the y(1) ion (38.4 kcal/mol), the former requires a tight transition state with an activation entropy, DeltaS++ = -1.2 cal/mol.K and the latter has a loose transition state with DeltaS++ = +8.8 cal/mol.K. This leads to y(1) being the major fragment ion over a wide energy range.     

Improved scalable syntheses of mono- and bis-urethane derivatives of ornithine

In the search for a practical route to ornithine bisurethane derivatives useful for peptide synthesis, we elaborated the simple and efficient (86% yield) synthesis of N(epsilon)-tert-butoxycarbonyl-L-ornithine copper(II) complex (1). This served as substrate for obtaining N(epsilon)-tert-butoxycarbonyl-L-ornithine (2), N(alpha)-benzyloxycarbonyl-N(epsilon)-tert-butoxycarbonyl-L-ornithine (3) and N(alpha)-(9-fluorenyl)methoxycarbonyl-N(epsilon)-tert-butoxycarbonyl-L-ornithine (4). These were synthesized in 94-95% yields and with a purity above 99%.     

Structures of protonated arginine dimer and bradykinin investigated by density functional theory: further support for stable gas-phase salt bridges

The gas-phase structures and energetics of both protonated arginine dimer and protonated bradykinin were investigated using a combination of molecular mechanics with conformational searching to identify candidate low-energy structures, and density functional theory for subsequent minimization and energy calculations. For protonated arginine dimer, a good correlation (R = 0.88) was obtained between the molecular mechanics and EDF1 6-31+G* energies, indicating that mechanics with MMFF is suitable for finding low-energy conformers. For this ion, the salt-bridge or ion-zwitterion form was found to be 5.7 and 7.2 kcal/mol more stable than the simple protonated or ion-molecule form at the EDF1 6-31++G** and B3LYP 6-311++G** levels. For bradykinin, the correlation between the molecular mechanics and DFT energies was poor (R = 0.28), indicating that many low-energy structures are likely passed over in the mechanics conformational searching. This result suggests that structures of this larger peptide ion obtained using mechanics calculations alone are not necessarily reliable. The lowest energy structure of the salt-bridge form of bradykinin is 10.6 kcal/mol lower in energy (EDF1) than the lowest energy simple protonated form at the 6-311G* level. Similarly, the average energy of all salt-bridge structures investigated is 13.6 kcal/mol lower than the average of all the protonated forms investigated. To the extent that a sufficient number of structures are investigated, these results provide some additional support for the salt-bridge form of bradykinin in the gas phase.     

Corannulene as a Lewis base: computational modeling of protonation and lithium cation binding.

A computational modeling of the protonation of corannulene at B3LYP/6-311G(d,p)//B3LYP/6-311G(d,p) and of the binding of lithium cations to corannulene at B3LYP/6-311G(d,p)//B3LYP/6-31G(d,p) has been performed. A proton attaches preferentially to one carbon atom, forming a sigma-complex. The isomer protonated at the innermost (hub) carbon has the best total energy. Protonation at the outermost (rim) carbon and at the intermediate (bridgehead rim) carbon is less favorable by ca. 2 and 14 kcal mol(-)(1), respectively. Hydrogen-bridged isomers are transition states between the sigma-complexes; the corresponding activation energies vary from 10 to 26 kcal mol(-)(1). With an empirical correction obtained from calculations on benzene, naphthalene, and azulene, the best estimate for the proton affinity of corannulene is 203 kcal mol(-)(1). The lithium cation positions itself preferentially over a ring. There is a small energetic preference for the 6-ring over the 5-ring binding (up to 2 kcal mol(-)(1)) and of the convex face over the concave face (3-5 kcal mol(-)(1)). The Li-bridged complexes are transition states between the pi-face complexes. Movement of the Li(+) cation over either face is facile, and the activation energy does not exceed 6 kcal mol(-)(1) on the convex face and 2.2 kcal mol(-)(1) on the concave face. In contrast, the transition of Li(+) around the corannulene edge involves a high activation barrier (24 kcal mol(-)(1) with respect to the lowest energy pi-face complex). An easier concave/convex transformation and vice versa is the bowl-to-bowl inversion with an activation energy of 7-12 kcal mol(-)(1). The computed binding energy of Li(+) to corannulene is 44 kcal mol(-)(1). Calculations of the (7)Li NMR chemical shifts and nuclear independent chemical shifts (NICS) have been performed to analyze the aromaticity of the corannulene rings and its changes upon protonation.     

Cyclization and rearrangement reactions of a(n) fragment ions of protonated peptides

a(n) ions are frequently formed in collision-induced dissociation (CID) of protonated peptides in tandem mass spectrometry (MS/MS) based sequencing experiments. These ions have generally been assumed to exist as immonium derivatives (-HN(+)═CHR). Using a quadrupole ion trap mass spectrometer, MS/MS experiments have been performed and the structure of a(n) ions formed from oligoglycines was probed by infrared spectroscopy. The structure and isomerization reactions of the same ions were studied using density functional theory. Overall, theory and infrared spectroscopy provide compelling evidence that a(n) ions undergo cyclization and/or rearrangement reactions, and the resulting structure(s) observed under our experimental conditions depends on the size (n). The a(2) ion (GG sequence) undergoes cyclization to form a 5-membered ring isomer. The a(3) ion (GGG sequence) undergoes cyclization initiated by nucleophilic attack of the carbonyl oxygen of the N-terminal glycine residue on the carbon center of the C-terminal immonium group forming a 7-membered ring isomer. The barrier to this reaction is comparatively low at 10.5 kcal mol(-1), and the resulting cyclic isomer (-5.4 kcal mol(-1)) is more energetically favorable than the linear form. The a(4) ion with the GGGG sequence undergoes head-to-tail cyclization via nucleophilic attack of the N-terminal amino group on the carbon center of the C-terminal immonium ion, forming an 11-membered macroring which contains a secondary amine and three trans amide bonds. Then an intermolecular proton transfer isomerizes the initially formed secondary amine moiety (-CH(2)-NH(2)(+)-CH(2)-NH-CO-) to form a new -CH(2)-NH-CH(2)-NH(2)(+)-CO- form. This structure is readily cleaved at the -CH(2)-NH(2)(+)- bond, leading to opening of the macrocycle and formation of a rearranged linear isomer with the H(2)C═NH(+)-CH(2)- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. This rearranged linear structure is much more energetically favorable (-14.0 kcal mol(-1)) than the initially formed imine-protonated linear a(4) ion structure. Furthermore, the barriers to these cyclization and ring-opening reactions are low (8-11 kcal mol(-1)), allowing facile formation of the rearranged linear species in the mass spectrometer. This finding is not limited to 'simple' glycine-containing systems, as evidenced by the IRMPD spectrum of the a(4) ion generated from protonated AAAAA, which shows a stronger tendency toward formation of the energetically favorable (-12.3 kcal mol(-1)) rearranged linear structure with the MeHC═NH(+)-CHMe- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. Our results indicate that one needs to consider a complex variety of cyclization and rearrangement reactions in order to decipher the structure and fragmentation pathways of peptide a(n) ions. The implications this potentially has for peptide sequencing are also discussed.     

Hydration of small peptides

The results for the sequential hydration of small peptides (<15 residues) obtained in our group are reviewed and put in perspective with other work published in the literature where appropriate. Our findings are based on hydration equilibrium measurements in a high-pressure drift cell inserted into an electrospray mass spectrometer and on calculations employing molecular mechanics and density functional theory methods. It is found that the ionic functional groups typically present in peptides, the ammonium, guanidinium, and carboxylate groups, are the primary target of water molecules binding to peptides. Whereas the water–guanidinium binding energy is fairly constant at 9 ± 1 kcal/mol, the water binding energy of an ammonium group ranges from 7 to 15 kcal/mol depending on how exposed the ammonium group is. A five-residue peptide containing an ammonium group is in favorable cases large enough to fully self-solvate the charge, but a pentapeptide containing a guanidinium group is too small to efficiently shield the charge of this much larger ionic group. The water–carboxylate interaction amounts to 13 kcal/mol with smaller values for a shielded carboxylate group. Both water bound to water in a second solvation shell and charge remote water molecules on the surface of the peptide are bound by 7–8 kcal/mol. The presence of several ionic groups in multiply charged peptides increases the number of favorable hydration sites, but does not enhance the water–peptide binding energy significantly. Water binding energies measured for the first four water molecules bound to protonated bradykinin do not show the declining trend typically observed for other peptides but are constant at 10 kcal/mol, a result consistent with a molecule containing a salt bridge with several good hydration sites. Questions regarding peptide structural changes as a function of number of solvating water molecules are discussed. Not much is known at present about the effect of individual water molecules on the conformation of peptides and on the stability of peptide zwitterions.     

Ab initio study of hydrogen-bond formation between aliphatic and phenolic hydroxy groups and selected amino acid side chains

Hydrogen bonding was studied in 24 pairs of isopropyl alcohol and phenol as one partner, and water and amino-acid mimics (methanol, acetamide, neutral and protonated imidazole, protonated methylalamine, methyl-guanidium cation, and acetate anion) as the other partner. MP2/6-31+G* and MP2/aug-cc-pvtz calculations were conducted in the gas phase and in a model continuum dielectric environment with dielectric constant of 15.0. Structures were optimized in the gas phase with both basis sets, and zero-point energies were calculated at the MP2/6-31+G* level. At the MP2/aug-cc-pvtz level, the BSSE values from the Boys-Bernardi counterpoise calculations amount to 10-20 and 5-10% of the uncorrected binding energies of the neutral and ionic complexes, respectively. The geometry distortion energy upon hydrogen-bond formation is up to 2 kcal/mol, with the exception of the most strongly bound complexes. The BSSE-corrected MP2/aug-cc-pvtz binding energy of -27.56 kcal/mol for the gas-phase acetate...phenol system has been classified as a short and strong hydrogen bond (SSHB). The CH3NH3+...isopropyl alcohol complex with binding energy of -22.54 kcal/mol approaches this classification. The complete basis set limit (CBS) for the binding energy was calculated for twelve and six complexes on the basis of standard and counterpoise-corrected geometry optimizations, respectively. The X...Y distances of the X-H...Y bridges differ by up to 0.03 A as calculated by the two methods, whereas the corresponding CBS energy values differ by up to 0.03 kcal/mol. Uncorrected MP2/aug-cc-pvtz hydrogen-bonding energies are more negative by up to 0.35 kcal/mol than the MP2/CBS values, and overestimate the CCSD(T)/CBS binding energies generally by up to 5% for the eight studied complexes in the gas phase. The uncorrected MP2/aug-cc-pvtz binding energies decreased (in absolute value) by 11-18 kcal/mol for the ionic species and by up to 5 kcal/mol for the neutral complexes when the electrostatic effect of a polarizable model environment was considered. The DeltaECCSD(T) - DeltaEMP2 corrections still remained close to their gas-phase values for four complexes with 0, +/-1 net charges. Good correlations (R2 = 0.918-0.958) for the in-environment MP2/aug-cc-pvtz and MP2/6-31+G* hydrogen-bonding energies facilitate the high-level prediction of these energies on the basis of relatively simple MP2/6-31+G* calculations.     

Intermolecular Mechanism and Dynamic Investigation of Avian Influenza H7N9 Virus’ Susceptibility to E119V-Substituted Peramivir–Neuraminidase Complex

The H7N9 virus attaches itself to the human cell receptor protein containing the polysaccharide that terminates with sialic acid. The mutation of neuraminidase at residue E119 has been explored experimentally. However, there is no adequate information on the substitution with E119V in peramivir at the intermolecular level. Therefore, a good knowledge of the interatomic interactions is a prerequisite in understanding its transmission mode and subsequent effective inhibitions of the sialic acid receptor cleavage by neuraminidase. Herein, we investigated the mechanism and dynamism on the susceptibility of the E119V mutation on the peramivir–neuraminidase complex relative to the wildtype complex at the intermolecular level. This study aims to investigate the impact of the 119V substitution on the neuraminidase–peramivir complex and unveil the residues responsible for the complex conformations. We employed molecular dynamic (MD) simulations and extensive post-MD analyses in the study. These extensive computational investigations were carried out on the wildtype and the E119V mutant complex of the protein for holistic insights in unveiling the effects of this mutation on the binding affinity and the conformational terrain of peramivir–neuraminidase E119V mutation. The calculated total binding energy (ΔG_bind) for the peramivir wildtype is −49.09 ± 0.13 kcal/mol, while the E119V mutant is −58.55 ± 0.15 kcal/mol. The increase in binding energy (9.46 kcal/mol) is consistent with other post-MD analyses results, confirming that E119V substitution confers a higher degree of stability on the protein complex. This study promises to proffer contributory insight and additional knowledge that would enhance future drug designs and help in the fight targeted at controlling the avian influenza H7N9 virus. Therefore, we suggest that experimentalists collaborate with computational chemists for all investigations of this topic, as we have done in our previous studies.     

Reactions of vinyl acetate and vinyl trifluoroacetate with cationic diimine Pd(II) and Ni(II) alkyl complexes: identification of problems connected with copolymerizations of these monomers with ethylene

Vinyl acetate (VA) and vinyl trifluoroacetate (VA(f)) react with [(NwedgeN)Pd(Me)(L)][X] (M = Pd, Ni, (NwedgeN) = N,N'-1,2-acenaphthylenediylidene bis(2,6-dimethyl aniline), Ar(f) = 3,5-trifluoromethyl phenyl, L = Ar(f)CN, Et2O; X = B(Ar(f))4-, SbF6-) to form pi-adducts 3 and 5 at -40 degrees C. Binding affinities relative to ethylene have been determined. Migratory insertion occurs in a 2,1 fashion (DeltaG++ = 19.4 kcal/mol, 0 degrees C for VA, and 17.4 kcal/mol, -40 degrees C for VA(f)) to yield five-membered chelate complexes [(NwedgeN)Pd(kappa2-CH(Et)(OC(O)-CH3))]+, 4, and [(NwedgeN)Pd(kappa2-CH(Et)(OC(O)CF3))]+, 6. When VA is added to [(NwedgeN)Ni(CH3)]+, an equilibrium mixture of an eta2 olefin complex, 8c, and a kappa-oxygen complex, 8o, results. Insertion occurs from the eta2 olefin complex, 8c (DeltaG++ = 15.5 kcal/mol, -51 degrees C), in both a 2,1 and a 1,2 fashion to generate a mixture of five- and six-membered chelates, 9(2,1) and 9(1,2). VA(f) inserts into the Ni-CH3 bond (-80 degrees C) to form a five-membered chelate with no detectable intermediate. Thermolysis of the Pd chelates results in beta-acetate elimination from 4 (DeltaG++ = 25.5 kcal/mol, 60 degrees C) and beta-trifluoroacetate elimination from 6 (DeltaG = 20.5 kcal/mol, 10 degrees C). The five-membered Ni chelate, 9(2,1), is quite stable at room temperature, but the six-membered chelate, 9(1,2), undergoes beta-elimination at -34 degrees C. Treatment of the OAc(f) containing Pd chelate 6 with ethylene results in complete opening to the pi-complex [(NwedgeN)Pd(kappa2-CH(Et)(OAc(f)))(CH2CH2)]+ (OAc(f) = OC(O)CF3), 18, while reaction of the OAc containing Pd chelate 4 with ethylene establishes an equilibrium between 4 and the open form 16, strongly favoring the closed chelate 4 (DeltaH = -4.1 kcal/mol, DeltaS = -23 eu, K = 0.009 M(-1) at 25 degrees C). The open chelates undergo migratory insertion at much slower rates relative to those of the simple (NwedgeN)Pd(CH3)(CH2CH2)+ analogue. These quantitative studies provide an explanation for the behavior of VA and VA(f) in attempted copolymerizations with ethylene.     

Reactions of hydrazoic acid on TiO2 nanoparticles: an experimental and computational study

This article reports the results of a computational and experimental study on the reaction of hydrazoic acid, HN3, adsorbed on 15-20 nm TiO2 particle films. Experimentally, FTIR spectra of HN3(a) have been measured by varying HN3 dosage, UV irradiation time and surface annealing temperature. Three sharp peaks, related to v(a)(NNN) of HN3(a) and N3(a) with different configurations in the 2000-2200 cm(-1) region, and a broad band absorption, related to associated and isolated HN(a) and HO(a) adsorptions in the 3000-3800 cm(-1) region, have been detected. Computationally, molecular structures, vibrational frequencies and adsorption energies of possible adsorbates including HN3 and its derivatives, N3, N2, NH, and H, have been predicted by first-principles calculations based on the density functional theory (DFT) and the pseudopotential method. On the basis of the experimental and computational results, the peak appeared at 2075 cm(-1), which increases at a faster rate with HN3 exposure time, is attributed to a stable adsorbate, N3-Ti(a), with the predicted adsorption energy, E(ads) = 13 kcal/mol. The peak at 2118 cm(-1), which survives at the highest surface temperature in the heating experiment, is attributable to the most stable adsorbate, Ti-N2N(H)-O(a) with E(ads) = 36 kcal/mol. The peak at 2170 cm(-1), which vanishes most readily in all of the aforementioned experiments, is related to less stable molecular adsorbates, end-on HN3-Ti(a) with E(ads) = 5 kcal/mol and side-on HN(N2)-Ti(a) with E(ads) = 8 kcal/mol. A potential energy diagram for the formation of various absorbates with their transition states has been established for the HN3/TiO2 system. On the basis of the predicted desorption energies, the four most stable products of the HN3 reaction on TiO2 are H-O(a), 118 kcal/mol; HN-O(a), 85 kcal/mol; Ti-N2N(H)-O(a), 36 kcal/mol; and N3-O(a), 19 kcal/mol.     

Sequential hydration of small protonated peptides

The sequential addition of water molecules to a series of small protonated peptides was studied by equilibrium experiments using electrospray ionization combined with drift cell techniques. The experimental data were compared to theoretical structures of selected hydrated species obtained by molecular mechanics simulations. The sequential water binding energies were measured to be of the order of 7-15 kcal/mol, with the largest values for the first water molecule adding to either a small nonarginine containing peptide (e.g., protonated dialanine) or to a larger peptide in a high charge state (e.g., triply protonated neurotensin). General trends are (a) that the first water molecules are more strongly bound than the following water molecules, (b) that very small peptides (2-3 residues) bind the first few water molecules more strongly than larger peptides, (c) that the first few water molecules bind more strongly to higher charge states than to lower charge states, and (d) that water binds less strongly to a protonated guanidino group (arginine containing peptides) than to a protonated amino group. Experimental differential entropies of hydration were found to be of the order of -20 cal/mol/K although values vary from system to system. At constant experimental conditions the number of water molecules adding to any peptide ion is strongly dependent on the peptide charge state (with higher charge states adding proportionally more water molecules) and only weakly dependent on the choice of peptide. For small peptides molecular mechanics calculations indicate that the first few water molecules add preferentially to the site of protonation until a complete solvation shell is formed around the charge. Subsequent water molecules add either to water molecules of the first solvation shell or add to charge remote functional groups of the peptide. In larger peptides, charge remote sites generally compete more effectively with charge proximate sites even for the first few water molecules.     

Complex formation of trimethylaluminum and trimethylgallium with ammonia: evidence for a hydrogen-bonded adduct

We have investigated the formation of gas-phase adducts of trimethylaluminum and trimethylgallium with ammonia using room-temperature Fourier transform infrared experiments and density functional theory calculations. Our results indicate for the first time that, at higher partial pressures, a product distinct from the well-known (CH3)3M:NH3 adduct grows in for both M = Al and M = Ga. Comparison of the experimental and calculated IR spectra, along with calculations of the energetics, indicates that this second product is the result of hydrogen bonding of a second NH3 molecule to the (CH3)3M:NH3 adduct and can be written as (CH3)3M:NH3...NH3. The binding energy of this hydrogen-bonded adduct is calculated to be 26.8 kcal/mol for M = Al and 18.4 kcal/mol for M = Ga and is lower in energy (more stable) relative to the 1:1 (CH3)3M:NH3 adduct by 7.2 kcal/mol for M = Al and 6.6 kcal/mol for M = Ga. In contrast, an alternative complex involving the formation of two separate M-N donor-acceptor bonds, which is written as H3N:(CH3)3M:NH3, is calculated to be lower in energy relative to (CH3)3M:NH3 by only 0.1 kcal/mol for M = Al and 0.2 kcal/mol for M = Ga and is not observed experimentally. These results show that hydrogen bonding plays an important role in the interaction of ammonia with metal organic precursors involving Al, Ga, and In, under typical metal organic chemical vapor deposition AlGaInN growth conditions.     

Structural Investigations and Binding Mechanisms of Oseltamivir Drug Resistance Conferred by the E119V Mutation in Influenza H7N9 Virus

The use of vaccinations and antiviral medications have gained popularity in the therapeutic management of avian influenza H7N9 virus lately. Antiviral medicines are more popular due to being readily available. The presence of the neuraminidase protein in the avian influenza H7N9 virus and its critical role in the cleavage of sialic acid have made it a target drug in the development of influenza virus drugs. Generally, the neuraminidase proteins have common conserved amino acid residues and any mutation that occurs around or within these conserved residues affects the susceptibility and replicability of the influenza H7N9 virus. Herein, we investigated the interatomic and intermolecular dynamic impacts of the experimentally reported E119V mutation on the oseltamivir resistance of the influenza H7N9 virus. We extensively employed molecular dynamic (MD) simulations and subsequent post-MD analyses to investigate the binding mechanisms of oseltamivir-neuraminidase wildtype and E119V mutant complexes. The results revealed that the oseltamivir-wildtype complex was more thermodynamically stable than the oseltamivir-E119V mutant complex. Oseltamivir exhibited a greater binding affinity for wildtype (−15.46 ± 0.23 kcal/mol) relative to the E119V mutant (−11.72 ± 0.21 kcal/mol). The decrease in binding affinity (−3.74 kcal/mol) was consistent with RMSD, RMSF, SASA, PCA, and hydrogen bonding profiles, confirming that the E119V mutation conferred lower conformational stability and weaker protein–ligand interactions. The findings of this oseltamivir-E119V mutation may further assist in the design of compounds to overcome E119V mutation in the treatment of influenza H7N9 virus patients.     

A novel tandem quadrupole mass spectrometer allowing gaseous collisional activation and surface induced dissociation.

A novel tandem quadrupole mass spectrometer is described that enables gaseous collision-induced dissociation (CID) and surface-induced dissociation (SID) experiments. The instrument consists of a commercially available triple quadrupole mass spectrometer connected to an SID region and an additional, orthogonal quadrupole mass analyser. The performance of the instrument was evaluated using leucine-enkephalin, allowing a comparison between CID and SID, and with previous reports of other SID instruments. The reproducibility of SID data was assessed by replicate determinations of the collision energy required for 50% dissociation of leucine-enkephalin; excellent precision was observed (standard deviation of 0.6 eV) though, unexpectedly, the reproducibility of the equivalent figure for CID was superior. Several peptides were analysed using SID in conjunction with liquid secondary-ion mass spectrometry or electrospray; a comparison of the fragmentation of singly protonated peptide ions and the further dissociation of y-type fragments was consistent with the equivalence of the latter fragments to protonated peptides. Few product ions attributable to high-energy cleavages of amino acid side-chains were observed. The SID properties were investigated of a series of peptides differing only in the derivatization of a cysteine residue; similar decomposition efficiencies were observed for all except the cysteic acid analogue, which demonstrated significantly more facile fragmentation.     

On the chaperon mechanism: application to ClO + ClO (+N2) --> ClOOCl (+N2)

The dynamics of the ClO + ClO (+N(2)) radical complex (or chaperon) mechanism is studied by electronic structure methods and quasi-classical trajectory calculations. The geometries and frequencies of the stationary points on the potential energy surface (PES) are optimized at the B3LYP/6-311+G(3df) level of theory, and the energies are refined at the CCSD(T)/6-311+G(3df) (single-point) level of theory. Basis set superposition error (BSSE) corrections are applied to obtain 1.5 kcal mol(-1) for the binding energy of the ClO.N(2) van der Waals (VDW) complex. A model PES is developed and used in quasi-classical trajectory calculations to obtain the capture rate constant and nascent energy distributions of ClOOCl* produced via the chaperon mechanism. A range of VDW binding energies from 1.5 to 9.0 kcal mol(-1) are investigated. The anisotropic PES for the ClO.N(2) complex and a separable anharmonic oscillator approximation are used to estimate the equilibrium constant for formation of the VDW complex. Rate constants, branching ratios to produce ClOOCl, and nascent energy distributions of excited ClOOCl* are discussed with respect to the VDW binding energy and temperature. Interestingly, even for weak VDW binding energies, the N(2) usually carries away enough energy to stabilize the nascent ClOOCl*, although the VDW equilibrium constant is small. For stronger binding energies, the stabilization efficiency is reduced, but the capture rate constant is increased commensurately. The resulting rate constants for forming ClOOCl* from the title reaction are only weakly dependent on the VDW binding energy and temperature. As a result, the relative importance of the chaperon mechanism is mostly dependent on the VDW equilibrium constant. For the calculated ClO.N(2) binding energy of 1.5 kcal mol(-1), the VDW equilibrium constant is small, and the chaperon mechanism is only important at very high pressures.     

Investigation of noncovalent interactions in deprotonated peptides: structural and energetic competition between aggregation and hydration

Noncovalent peptide-peptide and peptide-water interactions in small model systems were examined using an electrospray mass spectrometer equipped with a high-pressure drift cell. The results of these aggregation and hydration experiments were interpreted with the aid of molecular mechanics (MM) and density functional theory (DFT) calculations. The systems investigated include bare deprotonated monomers and dimers [P(1,2)-H](-) and hydrated deprotonated monomers and dimers [P(1,2)-H](-).(H(2)O)(n)() for the peptides dialanine (P = AA) and diglycine (P = GG). Mass spectra indicated that both peptides AA and GG form exclusively dimer ions in the electrospray process. Monomeric ions were generated by high-energy injection of the dimers into the drift cell. Temperature-dependent hydration equilibrium experiments carried out in the drift cell yielded water binding energies ranging from 11.7 (first water molecule) to 7.1 kcal/mol (fourth water) for [AA-H](-) and 11.0 to 7.4 kcal/mol for [GG-H](-). The first water molecule adding to the dimer ions [AA-H](-).(AA) and [GG-H](-).(GG) is bound by 8.4 and 7.5 kcal/mol, respectively. The hydration mass spectra for the monomers and dimers provide a means to compare the ability of water and a neutral peptide to solvate a deprotonated peptide [P-H](-). The data indicate that a similar degree of solvation is achieved by four water molecules, [P-H](-).(H(2)O)(4), or one neutral peptide, [P-H](-).(P). Temperature-dependent kinetics experiments yielded activation energies for dissociation of the dimers [AA-H](-).(AA) and [GG-H](-).(GG) of 34.9 and 32.2 kcal/mol, respectively. MM and DFT calculations carried out for the dialanine system indicated that the dimer binding energy is 24.3 kcal/mol, when the [AA-H](-) and AA products are relaxed to their global minimum structures. However, a value of 38.9 kcal/mol is obtained if [AA-H](-) and AA dissociate but retain the structures of the moieties in the dimer, suggesting the transition state occurs early in the dissociation process. Similar results were found for the diglycine dimer.