Facial selectivity of the (R)-1,3-dimethyl-1-cyclohexyl cation in the gas phase

The model reaction between the (R)-1,3-dimethyl-1-cyclohexyl cation (I) and methanol has been investigated under gas-phase radiolytic conditions (750 Torr; 25-120 degrees C) with the aim of evaluating the intrinsic factors that govern the facial selectivity of biased carbocations. The peculiarity of the experimental approach allows the formation of different CH(3) (18)OH.I ionic adducts. Subsequent conversion of these adducts to give the corresponding E/Z covalent products follows different reaction coordinates, which are characterized by their own activation parameters. On the grounds of density functional theory (DFT) results, several [CH(3)OH.I] structures have been located on the relevant potential-energy surface (PES). The experimental results point to a gas-phase facial selectivity, which is mainly governed by entropic factors that arise as a result of the occurrence of different noncovalent ion-molecule "facial adducts" (FA). The formation of FAs may also play an important role in both the reaction dynamics and the positional selectivity. The present results cannot be interpreted by any of the models based on solution-phase experiments.     

Geometric structure of molecule of 1,3-dinitro-1,3-diazacyclopentane in the gas phase

M. V. Lomonosov Moscow State University. Translated from Zhurnal Strukturnoi Khimii, Vol. 33, No. 1, pp. 35–40, January–February, 1992.     

Vibrational frequencies and structural determination of 1,6-dicarba-closo-hexaborane(6)

The normal mode frequencies and corresponding vibrational assignments of 1,6-dicarba-closo-hexaborane(6) are examined theoretically using the GAUSSIAN98 set of quantum chemistry codes. All normal modes were successfully assigned to one of six types of motion predicted by a group theoretical analysis (B-B stretch, B-C stretch, B-H stretch, C-H stretch, B-H bend, and C-H bend) utilizing the D(4h) symmetry of the molecule. The vibrational modes of the naturally isotopically substituted (1-(10)B, 2-(10)B 3-(10)B, and 4-(10)B) forms of 1,6-dicarba-closo-hexaborane(6) were also calculated and compared against experimental data. A complex pattern of frequency shifts and splittings is revealed.     

Kinetics and mechanism of the addition of 1,3-butadiene to cyclohexa-1,3-diene in the gas phase

The thermal reactions of 1,3-butadiene (BD) with cyclohexa-1,3-diene (CHD) have been studied in a static system between 437 and 526 K. The pressures of BD and CHD were varied from 61 to 397 torr and from 50 to 93 torr, respectively. The percentages of consumed BD and CHD were always kept lower than 14%. The reactions—in the order of importance—are All the reactions are homogeneous and of the first order with respect to the reagents. Their rate constants (in L/mol·s) are given by A thermochemical analysis of a biradical mechanism is in agreement with these results.     

Thermal dissociation of protein-oligosaccharide complexes in the gas phase: mapping the intrinsic intermolecular interactions

Blackbody infrared radiative dissociation (BIRD) and functional group replacement are used to map the location and strength of hydrogen bonds between an antibody single chain fragment (scFv) and its natural trisaccharide receptor, alpha-D-Galp (1-->2)[alpha-D-Abep (1-->3)]alpha-D-Manp1-->OMe (1), in the gaseous, multiply protonated complex. Arrhenius activation parameters (E(a) and A) are reported for the loss of 1 and a series of monodeoxy trisaccharide congeners (5-8 identical with tri) from the (scFv + tri + 10H)(+10) complex. The energetic contribution of the specific oligosaccharide OH groups to the stability of the (scFv + 1 + 10H)(+10) complex is determined from the differences in E(a) measured for the trisaccharide analogues and 1 (55.2 kcal/mol). A decrease of 6 to 11 kcal/mol in E(a), measured for the monodeoxy trisaccharides, indicates that the deleted OH groups interact strongly with the scFv and that they account for a majority of the stabilizing intermolecular interactions. A partial map of the hydrogen bond donor/acceptor groups of 1 and the strength of the interactions is presented for the protonated +10 complex. A comparison of the gas-phase map with the crystal structure indicates that significant structural differences exist. The hydroxyl groups located outside of the binding pocket, and exposed to solvent in solution, participate in new protein-oligosaccharide hydrogen bonds in the gas phase. The decrease in kinetic and energetic stability of the (scFv + 2 + nH)(n)()(+) complex with increasing charge-state is attributed to conformational differences in the binding region induced by electrostatic repulsion. The similarity in the Arrhenius parameters for the +9 and +10 charge states suggests that repulsion effects on the structure of the binding region are negligible below +11.     

Microwave spectra and gas phase structural parameters for N-hydroxypyridine-2(1H)-thione

The microwave spectrum for N-hydroxypyridine-2(1H)-thione (pyrithione) was measured in the frequency range 6-18 GHz, providing accurate rotational constants and nitrogen quadrupole coupling strengths for three isotopologues, C(5)H(4)(32)S(14)NOH, C(5)H(4)(32)S(14)NOD, and C(5)H(4)(34)S(14)NOH. Pyrithione was found to be in a higher concentration in the gas phase than the other tautomer, 2-mercaptopyridine-N-oxide (MPO). Microwave spectroscopy is best suited to determine which structure predominates in the gas phase. The measured rotational constants were used to accurately determine the coordinates of the substituted atoms and provided sufficient data to determine some of the important structural parameters for pyrithione, the only tautomer observed in the present work. The spectra were obtained using a pulsed-beam Fourier transform microwave spectrometer, with sufficient resolution to allow accurate measurements of the (14)N nuclear quadrupole hyperfine interactions. Ab initio calculations provided structural parameters and quadrupole coupling strengths that are in very good agreement with measured values. The experimental rotational constants for the parent compound are A = 3212.10(1), B = 1609.328(7), and C = 1072.208(6) MHz, yielding the inertial defect Δ(0) = -0.023 amu·?(2) for the C(5)H(4)(32)S(14)NOH isotopologue. The observed near zero inertial defect clearly indicates a planar structure. The least-squares fit structural analysis yielded the experimental bond lengths R(O-H) = 0.93(2) ?, R(C-S) = 1.66(2) ?, and angle (N-O-H) = 105(4)° for the ground state structure.     

Theoretical study of the structural,spectroscopic and energetic properties of difluoro(germylthio)phosphine and difluoro(germylseleno)phosphine in the gas phase

Theoretical methods have been employed to investigate the structural, spectroscopic and energetic properties of difluoro(germylthio)phosphine in the C_s symmetry in the gas phase. The levels of theory used are MP2 and DFT/B3LYP and the basis set used for all atoms is 6-311G(d,p). The computed structural parameters, namely, bond lengths and bond angles and spectroscopic parameters, namely, infrared frequencies, Raman activities and NMR chemical shifts have been compared with experimental data reported in literature. The structure of this compound has been analysed using natural bond orbital approach. Both the ab initio methods perform satisfactorily when the predicted and experimental parameters are compared. We have extended this study, using the same methods and basis set, to the selenium analogue, namely, difluoro(germylseleno)phosphine for which literature is elusive. The MP2/6-311G(d,p) geometrical parameters for difluoro(germylseleno)phosphine are: r(P–Se) = 2.270, r(Ge-Se) = 2.386, r(P–F) = 1.604, r(Ge–H) = 1.530 Å, ∠(Ge–Se–P) = 91.4, ∠(F–P–F) = 96.7, ∠(Se–P–F) = 99.9 and ∠(Se–Ge–H) = 109.5°. Apart from these, we have also studied the energetic parameters for their synthesis. The results indicate that formation of the sulphur-containing compound is favoured thermodynamically.     

Acidity and proton affinity of hypoxanthine in the gas phase versus in solution: intrinsic reactivity and biological implications

Hypoxanthine is a mutagenic purine base that most commonly arises from the oxidative deamination of adenine. Damaged bases such as hypoxanthine are associated with carcinogenesis and cell death. This inevitable damage is counteracted by glycosylase enzymes, which cleave damaged bases from DNA. Alkyladenine DNA glycosylase (AAG) is the enzyme responsible for excising hypoxanthine from DNA in humans. In an effort to understand the intrinsic properties of hypoxanthine, we examined the gas-phase acidity and proton affinity using quantum mechanical calculations and gas-phase mass spectrometric experimental methods. In this work, we establish that the most acidic site of hypoxanthine has a gas-phase acidity of 332 +/- 2 kcal mol-1, which is more acidic than hydrochloric acid. We also bracket a less acidic site of hypoxanthine at 368 +/- 3 kcal mol-1. We measure the proton affinity of the most basic site of hypoxanthine to be 222 +/- 3 kcal mol-1. DFT calculations of these values are consistent with the experimental data. We also use calculations to compare the acidic and basic properties of hypoxanthine with those of the normal bases adenine and guanine. We find that the N9-H of hypoxanthine is more acidic than that of adenine and guanine, pointing to a way that AAG could discriminate damaged bases from normal bases. We hypothesize that AAG may cleave certain damaged nucleobases as anions and that the active site may take advantage of a nonpolar environment to favor deprotonated hypoxanthine as a leaving group versus deprotonated adenine or guanine. We also show that an alternate mechanism involving preprotonation of hypoxanthine is energetically less attractive, because the proton affinity of hypoxanthine is less than that of adenine and guanine. Last, we compare the acidity in the gas phase versus that in solution and find that a nonpolar environment enhances the differences in acidity among hypoxanthine, adenine, and guanine.     

Metal-assisted esterification: glutaric acid-iron(II) complexes in the gas phase

Transition metal ions are routinely used to assist organic reactions; however, direct detection of the intermediates in such reactions is uncommon. Here, we demonstrate a transition metal ion-assisted reaction between glutaric acid (L) and methanol, using electrospray ionization mass spectrometry (ESI-MS). Esterification of glutaric acid does not occur in aqueous methanol solution under ESI conditions, but the FeII-bound acid cluster, [FeII L2 - H]+, adds methanol and dehydrates to give rise to an abundant product ion with a 14 Da increased mass. The occurrence of methyl esterification is supported by collision-induced dissociation and isotopic labeling data, which indicate that the sequence by which the product ion is generated is loss of water, followed by the addition of methanol. Electrospray ionization conditions, specifically the tube lens offset voltage, strongly affect the reaction efficiency, presumably through control of the dehydration process. Other transition metal ions, such as NiII, ZnII, CoII and CuII, also show distinctive metal-assisted reactions.     

Kinetics of the addition of propene to cyclohexa-1,3-diene in the gas phase

The addition of propene to cyclohexa-1,3-diene has been studied between 512 and 638°K at pressures between 70 and 640 torr. The products are endo- and exo-5-methylbicyclo [2.2.2] oct-2-ene, and their formations are second order. The rate constants (in 1./mole-sec) are given by The results are discussed in terms of a biradical mechanism.     

Probing the competition between secondary structures and local preferences in gas phase isolated peptide backbones

Combining laser desorption with a supersonic expansion together with the selectivity of IR/UV double resonance spectroscopy makes it possible to isolate and characterise the gas phase of remarkable backbone conformations of short peptide chains mimicking protein segments. A systematic bottom-up approach involving a conformer-specific IR study of peptide sequences of increasing sizes has enabled us to map the spectral signatures of the intramolecular interactions, which shape the peptide backbone, in particular H-bonds. The precise data collected are directly comparable to the most sophisticated quantum chemistry calculations of these species and therefore constitute a stringent test for the theoretical methods used. One-residue chains reveal the local conformational preference of the backbone and its dependence upon the nature of the residue. The investigation of longer chains provides evidence for a competition between simple successions of local conformational preferences along the chain and more folded structures, in which a new H-bonding network, involving distant H-bonding sites along the backbone, takes place. From three residues, the issue of helical folding can also be addressed. The present review of the gas phase literature data emphasizes the observation of remarkable secondary structures of biology, including short segments of beta-strands, gamma- and beta-turns, combinations of turns, including a 3(10) helix. It also provides evidence for the flexibility of the peptide chains, i.e., a critical influence of rather minor interactions (like side-chain/backbone interactions) on the conformational stability. Finally, the paper will discuss future promising directions of the present approach.     

Energetics and structural properties, in the gas phase, of trans-hydroxycinnamic acids

We have studied the energetics and structural properties of trans-cinnamic acid (CA), o-, m-, and p-coumaric acids (2-, 3-, and 4-hydroxycinnamic acids), caffeic acid (3,4-dihydroxycinnamic acid), ferulic acid (4-hydroxy-3-methoxycinnamic acid), iso-ferulic acid (3-hydroxy-4-methoxycinnamic acid), and sinapic acid (3,5-dimethoxy-4-hydroxycinnamic acid). The experimental values of Δ(f)H(m)°(g), determined (in kJ·mol(-1)) for CA (-229.8 ± 1.9), p-coumaric acid (-408.0 ± 4.4), caffeic acid (-580.0 ± 5.9), and ferulic acid (-566.4 ± 5.7), allowed us to derive Δ(f)H(m)°(g) of o-coumaric acid (-405.6 ± 4.4), m-coumaric acid (-406.4 ± 4.4), iso-ferulic acid (-565.2 ± 5.7), and sinapic acid (-698.8 ± 4.1). From these values and by use of isodesmic/homodesmotic reactions, we studied the energetic effects of π-donor substituents (-OH and -OCH(3)) in cinnamic acid derivatives and in the respective benzene analogues. Our results indicate that the interaction between -OCH(3) and/or -OH groups in hydroxycinnamic acids takes place without significant influence of the propenoic fragment.     

Chlorobis(pentafluoroethyl)phosphane: improved synthesis and molecular structure in the gas phase

(C₂F₅)₂PCl is now accessible through a significantly improved synthesis protocol starting from the technical product (C₂F₅)₃PF₂. (C₂F₅)₃PF₂ was reduced in the first step with NaBH₄ in a solvent‐free reaction at 120 °C. The product, P(C₂F₅)₃, was treated with an excess of an aqueous sodium hydroxide solution to afford the corresponding phosphinite salt Na⁺(C₂F₅)₂PO^? selectively under liberation of pentafluoroethane. Subsequent chlorination with PhPCl₄ resulted in the selective formation of (C₂F₅)₂PCl, which was isolated by fractional condensation in an overall yield of 66 %. The gas electron diffraction (GED) pattern for (C₂F₅)₂PCl was recorded and found to be described by a two‐conformer model. A quantum chemical investigation of the potential‐energy surface revealed the possible existence of many low‐energy conformers, each with a number of low‐frequency vibrational modes and therefore large‐amplitude motions. The conformer calculated to be most stable was also found to be most abundant by GED and comprised 61(5) % of the total. The molecular structure parameters determined by GED were in good agreement with those calculated at the MP2/TZVPP level of theory; the only significant difference was a discrepancy of about 3° in the C‐P‐C angle, which, for the lowest‐energy conformer, was refined to 98.2(4)° and was calculated to be 94.9°.     

Structures and hydration enthalpies of cationized glutamine and structural analogues in the gas phase

The structures of lithiated and sodiated glutamine, both with and without a water molecule, are investigated using experiment and theory. Loss of water from these complexes and from lithiated and sodiated complexes of asparagine methyl ester, asparagine ethyl ester, and glutamine methyl ester is probed with blackbody infrared radiative dissociation experiments performed over a wide temperature range. Threshold dissociation energies, E(o), for loss of a water molecule from these complexes are obtained from master equation modeling of these data. The values of E(o) are 63 +/- 1 and 53 +/- 1 kJ/mol for the lithiated and sodiated glutamine complexes, respectively. These values are similar to those for the nonzwitterionic model complexes and are in excellent agreement with calculated values. In contrast, water binding to the zwitterionic form is calculated to be significantly higher. These results indicate that glutamine in these lithiated and sodiated complexes with a water molecule are nonzwitterionic. Complexes with the asparagine side chain have slightly higher E(o) values than those with the glutamine side chain, a result consistent with more effective solvation of the metal ion due to the slightly longer side chain of glutamine. Calculations indicate that lithiated and sodiated glutamine are nonzwitterionic, with the metal ion interacting with the amine nitrogen and carbonyl oxygen from the amino acid backbone and the amide oxygen of the side chain. Addition of a water molecule does not affect the lowest-energy structure of lithiated glutamine, whereas, for sodiated glutamine, the lowest-energy zwitterionic and nonzwitterionic structures are essentially isoenergetic.     

Absolute potassium cation affinities (PCAs) in the gas phase

The potassium cation affinities (PCAs) of 136 ligands (20 classes) in the gas phase were established by hybrid density functional theory calculations (B3-LYP with the 6-311+G(3df,2p) basis set). For these 136 ligands, 70 experimental values are available for comparison. Except for five specific PCA values-those of phenylalanine, cytosine, guanine, adenine (kinetic-method measurement), and Me(2)SO (by high-pressure mass spectrometric equilibrium measurement)-our theoretical estimates and the experimental affinities are in excellent agreement (mean absolute deviation (MAD) of 4.5 kJ mol(-1)). Comparisons with previously reported theoretical PCAs are also made. The effect of substituents on the modes of binding and the PCAs of unsubstituted parent ligands are discussed. Linear relations between Li+/Na+ and K+ affinities suggest that for the wide range of ligands studied here, the nature of binding between the cations and a given ligand is similar, and this allows the estimation of PCAs from known Li+ and/or Na+ affinities. Furthermore, empirical equations relating the PCAs of ligands with their dipole moments, polarizabilities (or molecular weights), and the number of binding sites were established. Such equations offer a simple method for estimating the PCAs of ligands not included in the present study.     

DFT studies on tautomeric preferences of 1-(pyridin-2-yl)-4-(quinolin-2-yl)butane-2,3-dione in the gas phase and in solution

Density functional theory (DFT) calculations show that in vacuum such α-diketone as 1-(pyridin-2-yl)-4-(quinolin-2-yl)butane-2,3-dione is much less stable than its enolimine–enaminone ((1Z,3Z)-3-hydroxy-4-(pyridin-2-yl)-1-(quinolin-2(1H)-ylidene)but-3-en-2-one) and dienaminone tautomers ((1Z,3Z)-1-(pyridin-2-yl)-4-(quinolin-2-yl)buta-1,3-diene-2,3-diol). Other its tautomers (multiple basic and acidic centers in their molecules enable multiple proton transfer to take place) are even more labile. Strength of the intramolecular hydrogen bonds and aromatic character of the (quasi)rings [proved by the Harmonic Oscillator Model of Aromaticity (HOMA) index] in their molecules were found to be responsible for the observed tautomeric preferences. Polar and basic solvent disfavors and favors the enolimine and enaminone tautomers, respectively.     

Pyridinium N-heteroarylaminides: synthesis of N-heteroaryltetramines based on 1,6-bis(phenoxy)hexane and 1,3-bis(phenoxymethyl)benzene

The synthesis of a set of new N-heteroaryltetramines is reported. A regioselective alkylation on the N-exo nitrogen of pyridinium N-(heteroaryl)aminide with the corresponding tetrabromo compounds, followed by a clean N-N bond reduction of the corresponding tetra-salts, allowed an easy and general method to obtain N,N′,N″,N?-tetrakis(2-heteroaryl)tetramines.     

Microhydration of the magnesium(II) acetate cation in the gas phase

Electrospray ionization of aqueous solutions of magnesium(II) acetate leads to microhydrated magnesium acetate cations of the type [(CH(3)COO)(2m-1)Mg(m)(H(2)O)(n)](+) with m = 1-4 and n = 0-4, which are characterized by mass spectrometry and, for the cluster with three water molecules, also by infrared multiphoton dissociation spectroscopy. Density functional theory is used to determine the energies of microhydration for the mononuclear species [(CH(3)COO)Mg(H(2)O)(n)](+) with n = 0-6 and the associated changes in molecular structure. While bidentate coordination of the acetato ligand is generally preferred, at higher values of n, a switch to a monodentate coordination becomes energetically competitive.