Rapid probe of the nicotine spectra by high-resolution rotational spectroscopy

Nicotine has been investigated in the gas phase and two conformational forms were characterized through their rotational spectra. Two spectroscopic techniques have been used to obtain the spectra: a new design of broadband Fourier transform microwave (FTMW) spectroscopy with an in-phase/quadrature-phase-modulation passage-acquired-coherence technique (IMPACT) and narrowband FTMW spectroscopy with coaxially oriented beam-resonator arrangement (COBRA). The rotational, centrifugal distortion and hyperfine quadrupole coupling constants of two conformers of nicotine have been determined and found to be in N-methyl trans configurations with the pyridine and pyrrolidine rings perpendicular to one another. The quadrupole hyperfine structure originated by two (14)N nuclei has been completely resolved for both conformers and used for their unambiguous identification.     

Nitropyridines as 2π-Partners in 1,3-Dipolar Cycloadditions with N-Methyl Azomethine Ylide: An Easy Access to Condensed Pyrrolines

1,3-Dipolar cycloaddition reactions of 2-substituted 5-R-3-nitropyridines and isomeric 3-R-5-nitropyridines with N-methyl azomethine ylide were studied. The effect of the substituent at positions 2 and 5 of the pyridine ring on the possibility of the [3+2]-cycloaddition process was revealed. A number of new derivatives of pyrroline and pyrrolidine condensed with a pyridine ring were synthesized.     

Theoretical analysis of pyridine protonation in water clusters of increasing size.

The protonation of pyridine in water clusters as a function of the number of water molecules was theoretically analyzed as a prototypical case for the protonation of organic bases. We determined the variation of structural, bonding, and energetic properties on protonation, as well as the stabilization of the ionic species formed. Thus, we used supermolecular models in which pyridine interacts with clusters of up to five water molecules. For each complex, we determined the most stable unprotonated and protonated structures from a simulated annealing at the semi ab initio level. The structures were optimized at the B3LYP/cc-pVDZ level. We found that the hydroxyl group formed on protonation of pyridine abstracts a proton from the ortho-carbon atom of the pyridine ring. The "atoms in molecules" theory showed that this C-H group loses its covalent character. However, starting with clusters of four water molecules, the C-H bond recovers its covalent nature. This effect is associated with the presence of more than one ring between the water molecules and pyridine. These rings stabilize, by delocalization, the negative charge on the hydroxyl oxygen atom. Considering the protonation energy, we find that the protonated forms are increasingly stabilized with increasing size of the water cluster. When zero-point energy is included, the variation follows closely an exponential decrease with increasing number of water molecules. Analysis of the vibrational modes for the strongest bands in the IR spectra of the complexes suggests that the protonation of pyridine occurs by concerted proton transfers among the different water rings in the structure. Symmetric water stretching was found to be responsible for hydrogen transfer from the water molecule to the pyridine nitrogen atom.     

Mechanism of pyridine protonation in water clusters of increasing size

This work presents a theoretical mechanistic study of the protonation of pyridine in water clusters, at the B3LYP/cc-pVDZ theory level. Clusters from one to five water molecules were used. Starting from previously determined structures, the reaction paths for the protonation process were identified. For complexes of pyridine with water clusters of up to three water molecules just one transition state (TS) links the solvated and protonated forms. It is found that the activation energy decreases with the number of water molecules. For complexes of four and five water molecules two transition states are found. For four water molecules, the first TS links the starting solvated structure with a new, less stable, solvated form through a concerted proton transfer between a ring of water molecules. The second TS links the new solvated structure to the protonated form. Thus, protonation is a two-step process. For the five water molecules cluster, the new solvated structure is more stable than the starting one. This structure exhibits two double hydrogen bonds involving the pyridinic nitrogen and several water molecules. The second TS links the new structure with the protonated form. Now the process occurs in one step. In all cases considered, the proton transfers involve an interconversion between covalent and hydrogen bonds. For four and five water molecules, the second TS is structurally and energetically very close to the protonated form. As evidenced by the vibration frequencies, this is due to a flat potential energy hypersurface in the direction of the reaction coordinate. Determination of DeltaG at 298.15 K and 1 atm shows that the protonation of pyridine needs at least four water molecules to be spontaneous. The complex with five water molecules exhibits a large DeltaG. This value yields a pKa of 2.35, relatively close to the reported 5.21 for pyridine in water.     

Puckering transition of proline residue in water

The puckering transition of the proline residue with trans and cis prolyl peptide bonds was explored by optimizations along the torsion angle chi1 of the prolyl ring using quantum-chemical methods in water. By analyzing the potential energy surfaces and local minima in water, it is observed that the puckering transition of the proline residue proceeds from a down-puckered conformation to an up-puckered one and vice versa through the transition state with an envelope form having the N atom at the top of the envelope and not a planar one, as seen in the gas phase, although the backbone conformations are different in the gas phase and in water. The barriers to the puckering transition DeltaGup-->down are estimated to be 3.12 and 3.00 kcal/mol for trans and cis conformers at the B3LYP/6-311++G(d,p) level of theory in water, respectively, which are about 1.7 kcal/mol higher than those in the gas phase. Out of 2197 prolines from the 241 high-resolution PDB chains, four transition-state-like structures with the envelope ring puckering are identified. Three of them have the trans prolyl peptide bonds and one has the cis one. The favorable or steric interactions by neighboring residues may be responsible for the stabilization of these transition-state-like ring structures in the proteins.     

Site of protonation of nicotine and nornicotine in the gas phase: pyridine or pyrrolidine nitrogen?

The gas-phase basicities (GBs) of nornicotine, nicotine, and model pyrrolidines have been measured by FT-ICR. These experimental GBs are compared with those calculated (for the two sites of protonation in the case of nicotine and nornicotine) at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d,p) level, or those estimated from substituent effects on the GBs of 2-substituted pyrrolidines, 2-substituted N-methylpyrrolidines, and 3-substituted pyridines. It is found that, in contrast to the Nsp(3) protonation in water, in the gas phase nornicotine is protonated on the pyridine nitrogen, because the effects of an intramolecular CH.Nsp(3) hydrogen bond and of the polarizability of the 3-(pyrrolidin-2-yl) substituent add up on the Nsp(2) basicity, while the polarizability effect of the 2-(3-pyridyl) substituent on the Nsp(3) basicity is canceled by its field/inductive electron-withdrawing effect. The same structural effects operate on the Nsp(3) and Nsp(2) basicities of nicotine, but here, the polarizability effect of the methyl group puts the pyrrolidine nitrogen basicity very close to that of pyridine. Consequently, protonated nicotine is a mixture of the Nsp(3) and Nsp(2) protonated forms.     

Kinetic Control of Protonation in Electrospray Ionization

The site of protonation in a molecule can greatly affect the fragments observed in product ion MS/MS spectra. In electrospray positive ionization mass spectra, protonation usually occurs predominantly on the most basic site on the molecule to produce the thermodynamically favored protonated species. However, the literature is unclear whether liquid phase or gas phase thermodynamics has the greater influence. This paper describes the protonation and fragmentation behavior of crizotinib and two of its impurities. Crizotinib has two possible protonation sites, a pyridine nitrogen and a secondary amine, piperidine nitrogen; the former is the favored site in the gas phase and the latter the more favored site in the liquid phase. The impurities contain alkyl substitution on the piperidine nitrogen, producing tertiary amine species. Literature precedence suggests that in the liquid phase, the piperidine nitrogen is still the most basic site but, in the gas phase, the pyridine nitrogen and the piperidine nitrogen have very similar basicities. Fragmentation data for the three molecules suggest that the secondary and tertiary amines protonate preferentially and almost exclusively on different sites. We propose that the secondary amine protonates on the piperidine nitrogen (influenced by solution thermodynamics) and the two tertiary amine structures protonate on the pyridine nitrogen because of steric hindrance at the most basic site of the molecule, allowing kinetic control of the protonation process.     

Atypical protonation states in the active site of HIV-1 protease: a computational study

The HIV protease (HIVP) is a prominent example for successful structure-based drug design. Besides its pharmaceutical impact, it is a well-studied system for which, as experimentally evidenced, protonation changes in the active site occur upon ligand binding. Therefore, it serves as an ideal candidate for a case study using our newly developed partial charge model, which was optimized toward the application of Poisson-Boltzmann based pK(a) calculations. The charge model suggests reliably experimentally determined protonation states in the active site of HIVP. Furthermore, we perform pKa calculations for two HIVP complexes with novel types of inhibitors developed and synthesized in our group. For these complexes, no experimental knowledge about the protonation states is given. For one of the compounds, containing a central pyrrolidine ring, the calculations predict that both catalytic aspartates should be deprotonated upon ligand binding.     

Conformational profile of a proline-arginine hybrid

The intrinsic conformational preferences of a new nonproteinogenic amino acid have been explored by computational methods. This tailored molecule, named ((β)Pro)Arg, is conceived as a replacement for arginine in bioactive peptides when the stabilization of folded turn-like conformations is required. The new residue features a proline skeleton that bears the guanidilated side chain of arginine at the C(β) position of the five-membered pyrrolidine ring, in either a cis or a trans orientation with respect to the carboxylic acid. The conformational profiles of the N-acetyl-N'-methylamide derivatives of the cis and trans isomers of ((β)Pro)Arg have been examined in the gas phase and in solution by B3LYP/6-31+G(d,p) calculations and molecular dynamics simulations. The main conformational features of both isomers represent a balance between geometric restrictions imposed by the five-membered pyrrolidine ring and the ability of the guanidilated side chain to interact with the backbone through hydrogen bonds. Thus, both cis- and trans-((β)Pro)Arg exhibit a preference for the α(L) conformation as a consequence of the interactions established between the guanidinium moiety and the main-chain amide groups.     

密度泛函理论研究银上吸附对巯基吡啶的SERS化学增强效应

基于密度泛函理论计算和拉曼光谱理论分析,我们研究了对巯基吡啶(4MPY)分子的拉曼光谱和其在银上的表面增强拉曼光谱(SERS),并进一步探讨了SERS与界面吸附结构、异构化、质子化和氢键作用以及低能激发态的关系。首先,我们对两种分子异构体的相对稳定性和拉曼光谱进行了理论分析。在此基础上,进而研究了该分子与不同银簇作用时的拉曼光谱,结果表明,4MPY以巯基硫与银簇作用形成强的Ag―S键,导致拉曼光谱的线型不依赖于所选银簇的大小。接着我们考虑了吡啶氮端作用的两种情况。(1)当4MPY-银簇复合物同时以吡啶氮与水簇或水合质子簇形成氢键时,结果表明吡啶环的部分振动频率随氢键和质子化发生蓝移。(2)当考虑吡啶氮与银簇作用时,吡啶环三角畸变振动发生蓝移。上述情况不仅解释了实验观测的振动频率变化,而且表明了化学环境改变对相对拉曼强度的影响。最后,我们计算了当对巯基吡啶分子以单端或双端与银簇作用,在考虑激发光与低能激发态的能量匹配时,拉曼光谱强度与低能激发态的关系。计算结果表明,在双端吸附构型下,与吡啶氮成键的银簇受激发产生电荷转移态,不仅导致吡啶环v_(12)、v_1和v_(8a)振动的拉曼信号增强,而且选择性地增强吡啶环C―H面内对称弯曲振动v9a的拉曼信号。     

Two-dimensional infrared study of 3-azidopyridine as a potential spectroscopic reporter of protonation state

The lack of general spectroscopic probes that can be used in a range of systems to probe kinetics and dynamics is a major obstacle to the widespread application of two-dimensional infrared (2D IR) spectroscopy. We have studied 3-azidopyridine to characterize its potential as a probe of the protonation state of the pyridine ring. We find that the azido-stretching vibration is split by accidental Fermi resonance interactions with one or more overtones and combination states. Using 2D IR spectroscopy, we determine the state structure of the resulting eigenstates for complexes of 3-azidopyridine with formic acid and trifluoroacetic acid in which the pyridine ring is unprotonated and protonated, respectively. Based on the measurements, we develop a two-oscillator depurturbation model to determine the energies and couplings of the zeroth-order azido-stretching state and the perturbing dark state that couples to it. Based on these results, we conclude that the azido-stretching vibration is, in fact, sensitive to the protonation state of the pyridine shifting up in frequency by 8?cm(-1) in the complex with trifluoroacetic acid relative to the formic acid complex. These results suggest that, although 3-azidopyridine is not suitable as a spectroscopic probe, the approach of employing an organic azide as a remote probe of protonation state holds significant promise.     

Electronic excitations of green fluorescent proteins: modeling solvatochromatic shifts of red fluorescent protein chromophore model compound in aqueous solutions

While green fluorescent proteins (GFPs) have been widely used as tools in biochemistry, cell biology, and molecular genetics, novel red fluorescent proteins (RFPs) with red fluorescence emission have also been identified, as complements to the existing GFP technology. The unusual spectrophotometric and fluorescence properties of GFPs and RFPs are controlled by the protonation states and possibly cis/trans isomerization within their chromophores. In this work, we have investigated the electronic structures, liquid structures, and solvent shifts of the possible neutral and anionic protonated states and the cis/trans isomerization of a RFP chromophore model compound HBMPI in aqueous solutions. The calculations reproduced the experimental absorption solvatochromatic shifts of dilute HBMPI in water under neutral and anionic conditions. Unlike the GFP chromophore, the RFP chromophore model compound HBMPI in basic solution can only adopt a conformation where the C=C bond between the bridge group and the imidazolinone ring and the C-C bond between the imidazolinone and ethylene groups exist in cis and trans conformations, respectively. Moreover, the solvent-solute hydrogen-bonding interactions are found to contribute significantly to the total solvent shifts of pi-pi* excitations of aqueous HBMPI solutions, signifying the importance of protein environment in the determination of the conformation of the chromophores in red fluorescent proteins.     

Interference between the hydrogen bonds to the two rings of nicotine

The biochemical transport and binding of nicotine depends on the hydrogen bonding between water and binding site residues to the pyridine ring and the protonated pyrrolidinium ring. To test the independence of these two moderately separated hydrogen-bonding sites, we have calculated the structures of clusters of protonated nicotine with water and a bicarbonate anion, benzene, indole, or a second water molecule. Unprotonated nicotine-water clusters have also been studied for contrast. The potential energy surfaces are first explored with an intermolecular anisotropic atom-atom model potential. Full geometry optimizations are then carried out using density functional theory to include nonadditive terms in the interaction energies. The presence of the charge on the pyrrolidine nitrogen removes the conventional hydrogen-bonding site on the pyridine ring. The hydrogen-bond ability of this site is nearly recovered when the protonated pyrrolidinium ring is bound to a bicarbonate anion, whereas its interaction with benzene shows a much smaller effect. Indole appears to partially restore the hydrogen-bond ability of the pyridine nitrogen, although indole and benzene both pi-bond to the pyrrolidinium ring. A second hydrogen-bonding water produces a significant conformational distortion of the nicotine. This demonstrates the limitations of the conventional qualitative predictions of hydrogen bonding based on the independence of molecular fragments. It also provides benchmarks for the development of atomistic modeling of biochemical systems.     

Internal energy deposition in chemical ionization/tandem mass spectrometry

The efficiency of the collision-induced dissociation (CID) process as a function of the internal energy deposited into the ion during the ionization event was evaluated. (M + H)+ ions of pyrrole, pyrrolidine, pyridine and piperidine (five and six-membered ring heterocyclics) were generated by chemical ionization (CI). The internal energy of the ions was varied by using different reagent gases. Both high-energy (keV) and low-energy (eV) CID were performed on these ions. The experiments showed that the (M + H)+ ions of the five-membered ring compounds, pyrrole and pyrrolidine, have higher fragmentation efficiencies than the six-membered ring compounds, pyridine and piperidine. Fragmentation efficiencies in high-energy CID clearly correlate with the internal energy deposited by the ionization technique. Experiments showed that the low-energy CID process is more sensitive than high-energy CID to changes in internal energy.     

(4R)-4-Hydroxy-1-nitroso-l-proline: synthesis, X-ray structure, ab initio and conformational calculations

4-Hydroxy-l-proline, an amino acid, an important component of collagen, was transformed into its N-nitroso-derivative, (4R)-4-hydroxy-1-nitroso-l-proline, 1 by butylnitrite in the acidic medium. The structure is a cyclic hydroxy-N-nitrosoacid with the carboxyl and hydroxyl groups trans to each other. The carboxyl group is in the syn-conformation. In the structure, the neutral molecules are connected via classical intermolecular O-H?O hydrogen bonds involving the hydroxyl and carboxyl groups [O?O=2.6251(14) Å], and form chains along the a-axis direction. The chains are linked into sheets via O-H?O hydrogen bond, [O?O=2.6813(15) Å] with participation of oxygen atom of nitroso group. Ab initio calculations based on density functional theory at the B3LYP/6-311++G(d, p) level of theory were performed to analyze the influence of 4-hydroxy-l-proline (Hyp) nitrosation on the conformation of the synthesized N-nitroso-compound. The geometry optimization of 1 and initial 4-hydroxy-l-proline was carried out in the gas phase and in solution using the polarizable continuum model. The single-point calculation was performed for the crystal structure of 1. The most stable conformer of 1 is observed in an aqueous solution. In this state, the pyrrolidine ring adopts an envelope conformation, which is also maintained in the gas phase. The twisted conformation of the pyrrolidine ring is present in all states of Hyp and in the crystal structure of 1. In 1 the interchange of five-membered ring conformation in solution and in the gas phase in comparison with the crystal is accompanied by an increase of the dipole moment of the molecule, which is maximal in solution.     

Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solution

The conformational behavior of the title compounds has been investigated by Hartree-Fock, MP2, and DFT computations on the most significant structures related to variations of the backbone dihedral angles, cis/trans isomerism around the peptide bond, and diastereoisomeric puckering of the pyrrolidine ring. In vacuum the reversed gamma turn (gammal), characterized by an intramolecular hydrogen bridge, corresponds to the absolute energy minimum for both puckerings (up and down) of the pyrrolidine ring. An additional energy minimum is found in the helix region, but only for an up puckering of the pyrrolidine ring. When solvent effects are included by means of the polarizable continuum model the conformer observed experimentally in condensed phases becomes the absolute minimum. The down puckering is always favored over its up counterpart, albeit by different amounts (0.4-0.5 kcal/mol for helical structures and about 2 kcal/mol for gammal structures). In helical structures cis arrangements of the peptide bond are only slightly less stable than their trans counterparts. This is no longer true for gammal structures, because the formation of an intramolecular hydrogen bond is possible only for trans peptide bonds. In most cases, proline and hydroxyproline show the same general trends; however, the electronegative 4(R) substituent of hydroxyproline leads to a strong preference for up puckerings irrespective of the backbone conformation.     

Chiral amine–imine ligands based on trans-2,5-disubstituted pyrrolidines and their application in the palladium-catalyzed allylic alkylation

A series of amine–imine bidentate ligands based on a trans-2,5-disubstituted pyrrolidine and pyridine moieties have been prepared. The use of these ligands in the palladium-catalyzed allylic alkylation reaction of rac-(E)-1,3-diphenylprop-2-enyl acetate is reported. The results suggest that these ligands are good catalyst precursors for the reaction. Electronic modification on the pyridine ring of the ligands does not have a significant effect on the enantioselectivity of the reaction but does on the reaction rate, while structural modification on either the pyridine or the pyrrolidine moiety affords dramatic changes on the outcome of the stereochemistry. Evidence from various studies suggested that during the palladium-catalyzed allylic alkylation reaction, nucleophilic attack onto the 1,3-diphenylallyl moiety in the transition state occurs mainly trans to the pyridine ring of the less stable conformation of the palladium complexes.     

Direct hydroxylation of N-substituted [4,5-b]pyridines and imidazo[4,5-c]pyridines

It is shown that when N-methyl (or benzyl) derivatives of imidazo[4,5-b]pyridine and N-methyl-substituted derivatives of imidazo[4,5-c]pyridine are heated with alkalis, the imidazole ring is always hydroxylated to give the corresponding 2-imidazolones.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1252–1254, September, 1976.     

The nicotinic pharmacophore: thermodynamics of the hydrogen-bonding complexation of nicotine, nornicotine, and models

The thermodynamics of the hydrogen-bonding complexation of the acetylcholine agonists nicotine and nornicotine and of model pyridines, pyrrolidines, and N-methylpyrrolidines has been measured in CCl(4) by FTIR spectrometry toward a reference hydrogen-bond donor, 4-fluorophenol. Various methods are devised for measuring separately the hydrogen-bond acceptor strength of each nitrogen of nicotine and nornicotine: variation of the stoichiometry of complexation; correlations with electrostatic potentials on nitrogens and with substituent constants in the series of 3-substituted pyridines, 2-substituted pyrrolidines, and 2-substituted N-methylpyrrolidines; and linear free energy relationships between 4-fluorophenol and hydrogen fluoride hydrogen-bonded complexes. It is consistently found that nicotine and nornicotine have two active hydrogen-bond acceptor sites, the pyridine and pyrrolidine nitrogens, and that ca. 90% (for nicotine) and 80% (for nornicotine) of the 1:1 hydrogen-bonded complexes are formed to the pyridine nitrogen, although the pyrrolidine nitrogen is the first protonation site of nicotine and nornicotine in water. The low hydrogen-bond basicity of the pyrrolidine nitrogen in nicotine is mainly explained by the inductive electron-withdrawing and steric effects of the 2-(3-pyridyl) substituent. The partition of the Gibbs energy of the isomerism of complexation (AH...Nsp(2) <==> AH...Nsp(3)) into enthalpic and entropic contributions shows that the selectivity in favor of the pyridine nitrogen is driven by entropy. It is important to recognize the bifunctionality of nicotine in hydrogen bonding for understanding its lipophilicity and molecular recognition in non protonic media. When monoprotonated on their sp(3) nitrogen, nicotine and nornicotine keep, through their sp(2) nitrogen, a significant hydrogen-bond basicity which is greater than that of the ester group of acetylcholine.     

Conformational preferences of beta- and gamma-aminated proline analogues

Quantum mechanical calculations have been used to investigate how the incorporation of an amino group to the Cbeta- or Cgamma-positions of the pyrrolidine ring affects the intrinsic conformational properties of the proline. Specifically, a conformational study of the N-acetyl-N'-methylamide derivatives of four isomers of aminoproline, which differ not only in the beta- or gamma-position of the substituent but also in its cis or trans relative disposition, has been performed. To further understand the role of the intramolecular hydrogen bonds between the backbone carbonyl groups and the amino side group, a conformational study was also performed on the corresponding four analogues of (dimethylamino)proline. In addition, the effects of solvation on aminoproline and (dimethylamino)proline dipeptides have been evaluated using a self-consistent reaction field model, and considering four different solvents (carbon tetrachloride, chloroform, methanol and water). Results indicate that the incorporation of the amino substituent into the pyrrolidine ring affects the conformational properties, with backbone...side chain intramolecular hydrogen bonds detected when it is incorporated in a cis relative disposition. In general, the incorporation of the amino side group tends to stabilize those structures where the peptide bond involving the pyrrolidine nitrogen is arranged in cis. The aminoproline isomer with the substituent attached to the Cgamma-position with a cis relative disposition is the most stable in the gas phase and in chloroform, methanol and water solutions. Replacement of the amino side group by the dimethylamino substituent produces significant changes in the potential energy surfaces of the four investigated (dimethylamino)proline-containing dipeptides. Thus, these changes affect not only the number of minima, which increases considerably, but also the backbone and pseudorotational preferences. In spite of these effects, comparison of the conformational preferences, i.e., the more favored conformers, calculated for different isomers of aminoproline and (dimethylamino)proline dipeptides showed a high degree of consistency for the two families of compounds.