Experimental and Theoretical Investigation of the Proton-Bound Dimer of Lysine

The structure of the proton-bound lysine dimer has been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations. The structures of different possible isomers of the proton-bound lysine dimer have been optimized at the B3LYP/6-31 + G(d) level of theory and IR spectra calculated using the same computational method. Based on relative Gibbs free energies (298 K) calculated at the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d) level of theory, LL-CS01, and followed closely (1.1 kJ mol^–1) by LL-CS02 are the most stable non-zwitterionic isomers. At the MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + (d,p) levels of theory, isomer LL-CS02 is favored by 3.0 and 2.3 kJ mol^–1, respectively. The relative Gibbs free energies calculated by the aforementioned levels of theory for LL-CS01 and LL-CS02 are very close and strongly suggest that diagnostic vibrational signatures found in the IRMPD spectrum of the proton-bound dimer of lysine can be attributed to the existence of both isomers. LL-ZW01 is the most stable zwitterionic isomer, in which the zwitterionic structure of the neutral lysine is well stabilized by the protonated lysine moiety via a very strong intermolecular hydrogen bond. At the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d), MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + G(d,p) levels of theory, the most stable zwitterionic isomer (LL-ZW01) is less favored than LL-CS01 by 7.3, 4.1 and 2.3 kJ mol^–1, respectively. The experimental IRMPD spectrum also confirms that the proton-bound dimer of lysine largely exists as charge-solvated isomers. Investigation of zwitterionic and charge-solvated species of amino acids in the gas phase will aid in a further understanding of structure, property, and function of biological molecules.     

Probing Protonation Sites of Isolated Flavins Using IR Spectroscopy: From Lumichrome to the Cofactor Flavin Mononucleotide

Infrared spectra of the isolated protonated flavin molecules lumichrome, lumiflavin, riboflavin (vitamin B₂), and the biologically important cofactor flavin mononucleotide are measured in the fingerprint region (600–1850 cm^?1) by means of IR multiple‐photon dissociation (IRMPD) spectroscopy. Using density functional theory calculations, the geometries, relative energies, and linear IR absorption spectra of several low‐energy isomers are calculated. Comparison of the calculated IR spectra with the measured IRMPD spectra reveals that the N10 substituent on the isoalloxazine ring influences the protonation site of the flavin. Lumichrome, with a hydrogen substituent, is only stable as the N1‐protonated tautomer and protonates at N5 of the pyrazine ring. The presence of the ribityl unit in riboflavin leads to protonation at N1 of the pyrimidinedione moiety, and methyl substitution in lumiflavin stabilizes the tautomer that is protonated at O2. In contrast, flavin mononucleotide exists as both the O2‐ and N1‐protonated tautomers. The frequencies and relative intensities of the two C?O stretch vibrations in protonated flavins serve as reliable indicators for their protonation site.     

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.     

Infrared spectra of the protonated neurotransmitter histamine: competition between imidazolium and ammonium isomers in the gas phase

The infrared (IR) spectrum of protonated histamine (histamineH(+)) was recorded in the 575-1900 cm(-1) fingerprint range by means of IR multiple photon dissociation (IRMPD) spectroscopy. The IRMPD spectrum of mass-selected histamineH(+) ions was obtained in a Fourier transform ion cyclotron resonance mass spectrometer coupled to an electrospray ionization source and an IR free electron laser. A variety of isomers were identified and characterized by quantum chemical calculations at the B3LYP and MP2 levels of theory using the cc-pVDZ basis set. The low-energy isomers are derived from various favourable protonation sites--all of which are N atoms--and different orientations of the ethylamine side chain with respect to the heterocyclic imidazole ring. The measured IRMPD spectrum was monitored in the NH(3) loss channel and exhibits 14 bands in the investigated spectral range, which were assigned to vibrational transitions of the most stable isomer, denoted A. This imidazolium-type isomer A with protonation at the imidazole ring and gauche conformation of the ethylamine side chain is significantly stabilized by an intramolecular ionic Nπ-H(+)···Nα hydrogen bond to the ethylamino group. The slightly less stable ammonium-type isomer B with protonation at the ethylamino group is only a few kJ mol(-1) higher in energy and may also provide a minor contribution to the observed IRMPD spectrum. Isomer B is derived from A by simple proton transfer from imidazole to the ethylamino group along the intramolecular Nπ-H(+)···Nα hydrogen bond via a low barrier, which is calculated to be of the order of 5-15 kJ mol(-1). Significantly, the most stable structure of isolated histamineH(+) differs from that in the condensed phase by both the protonation site and the conformation of the side chain, emphasizing the important effects of solvation on the structure and function of this neurotransmitter. The effects of protonation on the geometric and electronic structure of histamine are evaluated by comparing the calculated properties of isomer A with those of the most stable structure of neutral histamine A(n).     

Modeling of protonation processes in acetohydroxamic acid

This work presents a theoretical study of acetohydroxamic acid and its protonation processes using ab initio methodology at the MP2(FC)/cc-pdVZ level. We find the amide form more stable than the imidic tautomer by less than 1.0 kcal mol(-)(1). For comparison with the experimental data, a three-dimensional conformational study is performed on the most stable tautomer (amide). From this study, the different barriers to rotation and inversion are determined and the intramolecular hydrogen bond between the OH group and the carbonyl oxygen is characterized. The electrostatic potential distribution shows three possible sites for electrophilic attack, but it is shown that only two of them, the carbonyl oxygen and the nitrogen atoms, are actual protonation sites. The protonation energy (proton affinity) is obtained from the results of the neutral and charged species. Proton affinities for the species charged on the carbonyl oxygen and the nitrogen atoms are estimated to be 203.4 and 194.5 kcal mol(-)(1), respectively. The development of a statistical model permits the quantification of DeltaG (gas-phase basicity) for the two protonation processes. In this way, the carbonyl oxygen protonated form is found to be more stable than that of the nitrogen atoms by 8.3 kcal mol(-)(1) at 1 atm and 298.15 K, due to the enthalpic contribution. As temperature increases, the proportion of the nitrogen protonated form increases slightly.     

Infrared spectroscopy of cationized lysine and epsilon-N-methyllysine in the gas phase: effects of alkali-metal ion size and proton affinity on zwitterion stability

The gas-phase structures of protonated and alkali-metal-cationized lysine (Lys) and epsilon-N-methyllysine (Lys(Me)) are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser, in conjunction with ab initio calculations. IRMPD spectra of Lys.Li(+) and Lys.Na(+) are similar, but the spectrum for Lys.K(+) is different, indicating that the structure of lysine in these complexes depends on the metal ion size. The carbonyl stretch of a carboxylic acid group is clearly observed in each of these spectra, indicating that lysine is nonzwitterionic in these complexes. A detailed comparison of these spectra to those calculated for candidate low-energy structures indicates that the bonding motif for the metal ion changes from tricoordinated for Li and Na to dicoordinated for K, clearly revealing the increased importance of hydrogen-bonding relative to metal ion solvation with increasing metal ion size. Spectra for Lys(Me).M(+) show that Lys(Me), an analogue of lysine whose side chain contains a secondary amine, is nonzwitterionic with Li and zwitterionic with K and both forms are present for Na. The proton affinity of Lys(Me) is 16 kJ/mol higher than that of Lys; the higher proton affinity of a secondary amine can result in its preferential protonation and stabilization of the zwitterionic form.     

Protonation Switching to the Least‐Basic Heteroatom of Carbamate through Cationic Hydrogen Bonding Promotes the Formation of Isocyanate Cations

We found that phenethylcarbamates that bear ortho‐salicylate as an ether group (carbamoyl salicylates) dramatically accelerate O?C bond dissociation in strong acid to facilitate generation of isocyanate cation (N‐protonated isocyanates), which undergo subsequent intramolecular aromatic electrophilic cyclization to give dihydroisoquinolones. To generate isocyanate cations from carbamates in acidic media as electrophiles for aromatic substitution, protonation at the ether oxygen, the least basic heteroatom, is essential to promote C?O bond cleavage. However, the carbonyl oxygen of carbamates, the most basic site, is protonated exclusively in strong acids. We found that the protonation site can be shifted to an alternative basic atom by linking methyl salicylate to the ether oxygen of carbamate. The methyl ester oxygen ortho to the phenolic (ether) oxygen of salicylate is as basic as the carbamate carbonyl oxygen, and we found that monoprotonation at the methyl ester oxygen in strong acid resulted in the formation of an intramolecular cationic hydrogen bond (>C?O⁺?H???O<) with the phenolic ether oxygen. This facilitates O?C bond dissociation of phenethylcarbamates, thereby promoting isocyanate cation formation. In contrast, superacid‐mediated diprotonation at the methyl ester oxygen of the salicylate and the carbonyl oxygen of the carbamate afforded a rather stable dication, which did not readily undergo C?O bond dissociation. This is an unprecedented and unknown case in which the monocation has greater reactivity than the dication.     

Stabilization of zwitterionic structures of amino acids (Gly, Ala, Val, Leu, Ile, Ser and Pro) by ammonium ions in the gas phase

The thermochemistry of gas-phase ion-molecule interactions and structures of a variety of clusters formed between protonated amino acids and either ammonia or amines have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. The enthalpy changes for the association reactions of protonated Gly, Ala, Val, Leu, Ile, Ser, and Pro with ammonia have been measured as -23.2, -21.9, -21.0, -20.8, -20.6, -22.6, and -20.4 kcal mol(-1), respectively. A very good linear relationship exists between the enthalpy changes and the proton affinities (PAs) of the amino acids, with an exception of Ser, where the hydroxyl substituent forms an extra hydrogen bond with ammonia. For the association reaction of protonated proline and methylamine, the measured enthalpy and entropy changes are -26.6 kcal mol(-1) and -30.1 cal mol(-1) K(-1), respectively. The experimental and calculated results indicate that the zwitterionic structure of proline may be well stabilized by CH3NH3(+). For the first time, the interaction strengths between these amino acids and NH4(+) have been obtained, and comparison with Na+ is discussed. Stabilization of zwitterionic structures of a series of amino acids (Gly, Ala, Val, Ser, and Pro) by various ammonium ions (NH4(+), CH3NH3(+), (CH3)2NH2(+), and (CH3)3NH+) has been investigated systematically. Energy decomposition analysis has been performed so that the salt bridge interaction strengths between zwitterionic amino acids and ammonium ions have been obtained. Some generalizations with respect to the relative stability of zwitterionic structures may be drawn. First, as the PA of an amino acid increases, within a series of Gly, Ala, Val, the zwitterionic structure becomes more energetically favorable relative to a non-zwitterionic isomer. Second, as the PA of an amine increases, the zwitterionic structure of a given amino acid within the complex becomes gradually less favorable. Third, compared to the other amino acids, Pro, the only secondary amine among the 20 naturally occurring amino acids, has a much more pronounced tendency to form the zwitterionic structure, which has been confirmed by the experimental results. Finally, substituents on the amino acid backbone that may participate in additional hydrogen bond interactions in non-zwitterionic isomer may render it more stable, as seen in Ser. These organic ammonium ions are found to be able to very effectively stabilize the zwitterionic structure of amino acids, even more effectively than metal ions, which aids significantly in the understanding of why zwitterionic structures exist extensively in biological systems.     

Tetramethyl‐m‐benziporphodimethene and Isomeric α,β‐Unsaturated γ‐Lactam Embedded N‐Confused Tetramethyl‐m‐benziporphodimethenes

The condensation reaction of α,α′‐dihydroxy‐1,3‐diisopropylbenzene, pyrrole, and an aldehyde leads to the formation of tetramethyl‐m‐benziporphodimethene and outer α‐pyrrolic carbon oxygenated N‐confused tetramethyl‐m‐benziporphodimethenes containing a γ‐lactam ring in the macrocycle. Two isomers with the carbonyl group of the lactam ring either close to (O‐Up) or away from (O‐Down) the neighboring sp³ meso carbon were synthesized and characterized. The single crystal X‐ray diffraction analysis on the regular and γ‐lactam containing tetramethyl‐m‐benziporphodimethenes showed highly distorted macrocycles for all compounds. For O‐Up and O‐Down isomers, dimeric structures, assembling by intermolecular hydrogen‐bonding interactions through lactam rings, were observed in the solid state. Fitting the concentration dependent chemical shifts of the outer NH proton using the non‐linear regression method give a maximum association constant of 108.9 M ^?1 for the meso 4‐methylcarboxyphenyl substituted O‐Down isomer. The DFT calculations concluded that the O‐Up isomer is energetically more stable, and the keto form is more stable than the enol form.     

Interactions of mono- and divalent metal ions with aspartic and glutamic acid investigated with IR photodissociation spectroscopy and theory

The interaction of metal ions with aspartic (Asp) and glutamic (Glu) acid and the role of gas-phase acidity on zwitterionic stability were investigated using infrared photodissociation spectroscopy in the spectral range 950-1900 cm (-1) and by hybrid density functional theory. Lithium ions interact with both carbonyl oxygen atoms and the amine nitrogen for both amino acids, whereas cesium interacts with both of the oxygen atoms of the C-terminus and the carbonyl oxygen of the side chain for Asp. For Glu, this structure is competitive, but a structure in which the cesium ion interacts with just the carbonyl oxygen atoms is favored and the calculated spectrum for this structure is more consistent with the experimentally measured spectrum. In complexes with either of these metal ions, both amino acids are non-zwitterionic. In contrast, Glu*Ca (2+) and Glu*Ba (2+) both adopt structures in which Glu is zwitterionic and the metal ion interacts with both oxygens of the C-terminal carboxylate and the carbonyl oxygen in the side chain. Assignment of the zwitterionic form of Glu is strengthened by comparisons to the spectrum of the protonated form, which indicate spectral features associated with a protonated amino nitrogen. Comparisons with results for glutamine, which adopts nearly the same structures with these metal ions, indicate that the lower Delta H acid of Asp and Glu relative to other amino acids does not result in greater relative stability of the zwitterionic form, a result that is directly attributed to effects of the metal ions which disrupt the strong interaction between the carboxylic acid groups in the isolated, deprotonated forms of these amino acids.     

On the Use of a Protic Ionic Liquid with a Novel Cation To Study Anion Basicity

The need for reliable means of ordering and quantifying the Lewis basicity of anions is discussed and the currently available methods are reviewed. Concluding that there is need for a simple impurity‐insensitive tool, we have sought, and here describe, a new method using NMR spectroscopy of a weak base, a substituted urea, 1,3‐dimethyl‐2‐imidazolidinone (DMI), as it is protonated by Brønsted acids of different strengths and characters. In all cases studied the product of protonation is a liquid (hence a protic ionic liquid). NMR spectroscopy detects changes in the electronic structure of the base upon interaction with the proton donors. As the proton‐donating ability, that is, acidity, increases, there is a smooth but distinct transition from a hydrogen‐bonded system (with no net proton transfer) to full ionicity. The liquid state of the samples and high concentration of nitrogen atoms, despite the very low natural abundance of its preferred NMR‐active isotope (¹⁵N), make possible the acquisition of ¹⁵N spectra in a relatively short time. These ¹⁵N, along with ¹³C, chemical shifts of the carbonyl atom, and their relative responses to protonation of the carbonyl oxygen, can be used as a means, sensitive to anion basicity and relatively insensitive to impurities, to sort anions in order of increasing hydrogen bond basicity. The order is found to be as follows: SbF₆^?<BF₄^?<NTf₂^?>ClO₄^?>FSO₃^?<TfO^?<HSO₄^?<Cl^?<MsO^?.     

Alkali metal ion binding to glutamine and glutamine derivatives investigated by infrared action spectroscopy and theory

The gas-phase structures of alkali-metal cationized glutamine are investigated by using both infrared multiple photon dissociation (IRMPD) action spectroscopy, utilizing light generated by a free electron laser, and theory. The IRMPD spectra contain many similarities that are most consistent with glutamine adopting nonzwitterionic forms in all ions, but differences in the spectra indicate that the specific nonzwitterionic forms adopted depend on metal-ion identity. For ions containing small alkali metals, the metal ion is solvated predominantly by the amino group, the carbonyl oxygen of the carboxylic acid group, and the carbonyl oxygen of the amide group. With increasing alkali-metal-ion size, additional structures are present in which the carboxylic acid group donates a hydrogen bond to the amino group and the metal ion is solvated only by the amide and carboxylic acid groups. The effects of alkylation of the amino and amide groups on the proton affinity of isolated glutamine and the relative zwitterion stability of sodiated glutamine were examined computationally. Methylation of the amino group increases the proton affinity of isolated glutamine and preferentially stabilizes the zwitterionic form of sodiated glutamine by roughly 20 kJ/mol. Ethylation and isopropylation of the amide group each increase the proton affinity of isolated glutamine by roughly 13 kJ/mol but preferentially stabilize the zwitterionic form of sodiated glutamine by less than 3 kJ/mol. These results indicate that effects of proton affinity on relative zwitterion stability compete with effects of metal-ion solvation.     

Structures of lithiated lysine and structural analogues in the gas phase: effects of water and proton affinity on zwitterionic stability

The structures of lithiated lysine, ornithine, and related molecules, both with and without a water molecule, are investigated using both density functional theory and blackbody infrared radiative dissociation experiments. The lowest-energy structure of lithiated lysine without a water molecule is nonzwitterionic; the metal ion interacts with both nitrogen atoms and the carbonyl oxygen. Structures in which lysine is zwitterionic are higher in energy by more than 29 kJ/mol. In contrast, the singly hydrated clusters with the zwitterionic and nonzwitterionic forms of lysine are more similar in energy, with the nonzwitterionic form more stable by only approximately 7 kJ/mol. Thus, a single water molecule can substantially stabilize the zwitterionic form of an amino acid. Analogous molecules that have methyl groups attached to either the N-terminus (NMeLys) or the side-chain amine (Lys(Me)) have proton affinities greater than that of lysine. In the lithiated clusters with a water molecule attached, the zwitterionic forms of NMeLys and Lys(Me) are calculated to be approximately 4 and approximately 11 kJ/mol more stable than the nonzwitterionic forms, respectively. Calculations of the potential-energy pathway for interconversion between the different forms of lysine in the lithiated complex indicate multiple stable intermediates with an overall barrier height of approximately 83 kJ/mol between the lowest-energy nonzwitterionic form and the most accessible zwitterionic form. Experimentally determined binding energies of water are similar for all these complexes and range from 57 to 64 kJ/mol. These results suggest that loss of a water molecule from the lysine complexes is both energetically and entropically favored compared to interconversion between the nonzwitterionic and zwitterionic structures. Comparisons to calculated binding energies of water to the various structures show that the experimental results are most consistent with the nonzwitterionic forms.     

Gas-phase properties and Fukui indices of sulfine (CH2SO). Potential energy surface and maximum hardness principle for its protonation process. A density functional study

Gas-phase thermochemical properties of sulfine (CH₂SO) and the potential energy surface of its protonation process were studied by the density functional method employing different exchange-correlation potentials. All calculations showed that the most stable protonated isomer is planar with the proton bonded to the oxygen atom in a trans arrangement of the skeleton. Three transition states were located that allow interconversion between the different isomers. Hardnesses and Fukui indices were calculated to follow the reactivity trend along the protonation path and to explain the preference for a particular protonation site on neutral sulfine. Proton affinity, gas-phase basicity and heat of formation values, obtained for the first time fully quantum mechanically, agree well with those derived by a recent mass spectrometry experimental study. Good agreement between density functional theory and previous high-level theoretical and experimental data was also found for the heat of formation of sulfine and its most stable protonated form. Received: 12 October 1998 / Accepted: 24 November 1998 / Published online: 16 March 1999     

Structural characterizations of protonated homodimers of amino acids: Revealed by infrared multiple photon dissociation (IRMPD) spectroscopy and theoretical calculations

Photon affinity can serve as a probe for predicting the structures of protonated homodimers of amino acids.     

Structure and Reactivity of the Distonic and Aromatic Radical Cations of Tryptophan

In this work, we regiospecifically generate and compare the gas-phase properties of two isomeric forms of tryptophan radical cations—a distonic indolyl N-radical (H₃N⁺ - TrpN^?) and a canonical aromatic π (Trp^?+) radical cation. The distonic radical cation was generated by nitrosylating the indole nitrogen of tryptophan in solution followed by collision-induced dissociation (CID) of the resulting protonated N-nitroso tryptophan. The π-radical cation was produced via CID of the ternary [Cu^II(terpy)(Trp)] ^?2+ complex. CID spectra of the two isomeric species were found to be very different, suggesting no interconversion between the isomers. In gas-phase ion-molecule reactions, the distonic radical cation was unreactive towards n-propylsulfide, whereas the π radical cation reacted by hydrogen atom abstraction. DFT calculations revealed that the distonic indolyl radical cation is about 82 kJ/mol higher in energy than the π radical cation of tryptophan. The low reactivity of the distonic nitrogen radical cation was explained by spin delocalization of the radical over the aromatic ring and the remote, localized charge (at the amino nitrogen). The lack of interconversion between the isomers under both trapping and CID conditions was explained by the high rearrangement barrier of ca.137 kJ/mol. Finally, the two isomers were characterized by infrared multiple-photon dissociation (IRMPD) spectroscopy in the ~1000–1800 cm^–1 region. It was found that some of the main experimental IR features overlap between the two species, making their distinction by IRMPD spectroscopy in this region problematic. In addition, DFT theoretical calculations showed that the IR spectra are strongly conformation-dependent.      

Density functional study of protonation sites of α‐Keggin isopolyanions

Density functional theory (DFT) calculations were carried out to characterize the optimal site of the protons and the precise protonation state in the polyoxometalate (POM) anions [V₁₃O₄₀]^15? and [H₁₂V₁₃O₄₀]^3?. Six kinds of possible protonated stable isomers with the whole Keggin anion units are discussed. The calculations reveal that the preferred protonation site corresponds to bridging oxygens that belong to the same trimetallic group (isomers B and C). Both isomers B and C are comparatively stable in the gas phase, but only isomer B could exist stably in aqueous solution because of being stabilized by the electrostatic interaction. The solvent effects and protonation are also discussed. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Tridentate ionic hydrogen-bonding interactions of the 5-fluorocytosine cationic dimer and other 5-fluorocytosine analogues characterized by IRMPD spectroscopy and electronic structure calculations

Ionic hydrogen-bonding interactions have been found in several clusters formed by 5-fluorocytosine (5-FC). The chloride and trimethylammonium cluster ions, along with the cationic (proton-bound) dimer have been characterized by infrared multiple-photon dissociation (IRMPD) spectroscopy and electronic structure calculations performed at the B2PLYP/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. IRMPD action spectra, in combination with calculated spectra and relative energetics, indicate that it is most probable that predominantly a single isomer exists in each experiment. For the 5-FC-trimethylammonium cluster specifically, the calculated spectrum of the lowest-energy isomer convincingly matches the experimental spectrum. Interestingly, the cationic dimer of 5-FC was found to have a single energetically relevant isomer (Cationic-IV) involving a tridentate ionic hydrogen-bonding interaction. The three sites of intermolecular ionic hydrogen bonds in this isomer interact very efficiently, leading to a significant calculated binding energy of 180 kJ/mol. The magnitude of the calculated binding energy for this species, in combination with the strong correlation between the simulated and IRMPD spectra, suggests that a tridentate-proton-bound dimer was observed predominantly in the experiments. Comparison of the calculated relative Gibbs free energies (298 K) for this species and several of the other isomers considered also supports the likelihood of the dominant protonated dimer existing as Cationic-IV.     

Protonation Preferentially Stabilizes Minor Tautomers of the Halouracils: IRMPD Action Spectroscopy and Theoretical Studies

Tautomerization induced by protonation of halouracils may increase their efficacy as anti-cancer drugs by altering their reactivity and hydrogen bonding characteristics, potentially inducing errors during DNA and RNA replication. The gas-phase structures of protonated complexes of five halouracils, including 5-fluorouracil, 5-chlorouracil, 5-bromouracil, 5-iodouracil, and 6-chlorouracil are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. IRMPD action spectra were measured for each complex in the IR fingerprint region extending from ~1000 to 1900?cm(-1) using the free electron laser (FELIX). Correlations are made between the measured IRMPD action spectra and the linear IR spectra for the stable low-energy tautomeric conformations computed at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G* level of theory. Absence of an intense band(s) in the IRMPD spectrum arising from the carbonyl stretch(es) that are expected to appear near 1825?cm(-1) provides evidence that protonation induces tautomerization and preferentially stabilizes alternative, noncanonical tautomers of these halouracils where both keto functionalities are converted to hydroxyl groups upon binding of a proton. The weak, but measurable absorption, which does occur for these systems near 1835?cm(-1) suggests that in addition to the ground-state conformer, very minor populations of excited, low-energy conformers that contain keto functionalities are also present in these experiments.     

Infrared spectra of protonated neurotransmitters: dopamine

The infrared (IR) spectrum of the isolated protonated neurotransmitter dopamine was recorded in the fingerprint range (570-1880 cm(-1)) by means of IR multiple photon dissociation (IRMPD) spectroscopy. The spectrum was obtained in a Fourier transform ion cyclotron resonance mass spectrometer equipped with an electrospray ionization source, which was coupled to a free electron laser (FEL). The spectroscopic studies are complemented by quantum chemical calculations at the B3LYP and MP2 levels of theory using the cc-pVDZ basis set. Several low-energy isomers with protonation occurring at the amino group are predicted in the energy range 0-50 kJ mol(-1). Good agreement between the measured IRMPD spectrum and the calculated linear absorption spectra is observed for the two gauche conformers lowest in energy (ΔE) and free energy (ΔG) at both levels of theory, denoted g-1 and g+1. Minor contributions of higher lying gauche isomers cannot be ruled out spectroscopically but their calculated energies suggest only minor population in the sampled ion cloud. In all these gauche structures, one of the three protons of the ammonium group is pointing toward the catechol subunit, thereby maximizing the intramolecular NH-π interaction of the positive charge with the aromatic ring. In total, 16 distinct vibrational bands are observed in the IRMPD spectrum and assigned to individual normal modes of the energetically most stable g-1 conformer, with deviations of less than 24 cm(-1) (average 11 cm(-1)) between measured and calculated frequencies. Comparison with neutral dopamine reveals the effects of protonation on the geometric and electronic structure.