A theoretical investigation of the low energy conformers of the isomers glycine and methylcarbamic acid and their role in the interstellar medium

We have theoretically investigated the low energy conformers of neutral glycine (NH(2)CH(2)COOH) and its isomer methylcarbamic acid (CH(3)NHCOOH) in the gas phase. A total of 16 different levels of the theory, including CCSD(T), MP2 and B3LYP methods with various Pople and Dunning type basis sets with and without polarization and diffuse functions were used. We found eight low energy glycine conformers, where the heavy atoms in three have a planar backbone, and four low energy methylcarbamic acid conformers all with non-planar backbones. Interestingly at all levels of theory, we found that the most stable methylcarbamic acid conformer is significantly lower in energy than the lowest energy glycine conformer. The MP2 level and single point CCSD(T) calculations show the lowest energy methylcarbamic acid conformer to be between 31 to 37 kJ mol(-1) lower in energy than the lowest energy glycine conformer. These calculations suggest that methylcarbamic acid might serve as a precursor to glycine formation in the Interstellar Medium (ISM). We also report the theoretical harmonic vibrational frequencies, infrared intensities, moment of inertia, rotational constants and dipole moments for all of the conformers. In order to understand how glycine or methylcarbamic acid might be formed in the ISM, larger calculations which model glycine or its isomer interacting with several surrounding molecules, such as water, are needed. We demonstrate that B3LYP method should provide a reliable and computationally practical approach to modeling these larger systems.     

A computational study on the structures of methylamine-carbon dioxide-water clusters: evidence for the barrier free formation of the methylcarbamic acid zwitterion (CH3NH2+COO-) in interstellar water ices

We investigated theoretically the interaction between methylamine (CH(3)NH(2)) and carbon dioxide (CO(2)) in the presence of water (H(2)O) molecules thus simulating the geometries of various methylamine-carbon dioxide complexes (CH(3)NH(2)/CO(2)) relevant to the chemical processing of icy grains in the interstellar medium (ISM). Two approaches were followed. In the amorphous water phase approach, structures of methylamine-carbon dioxide-water [CH(3)NH(2)/CO(2)/(H(2)O)(n)] clusters (n = 0-20) were studied using density functional theory (DFT). In the crystalline water approach, we simulated methylamine and carbon dioxide interactions on a fragment of the crystalline water ice surface in the presence of additional water molecules in the CH(3)NH(2)/CO(2) environment using DFT and effective fragment potentials (EFP). Both the geometry optimization and vibrational frequency analysis results obtained from these two approaches suggested that the surrounding water molecules which form hydrogen bonds with the CH(3)NH(2)/CO(2) complex draw the carbon dioxide closer to the methylamine. This enables, when two or more water molecules are present, an electron transfer from methylamine to carbon dioxide to form the methylcarbamic acid zwitterion, CH(3)NH(2)(+)CO(2)(-), in which the carbon dioxide is bent. Our calculations show that the zwitterion is formed without involving any electronic excitation on the ground state surface; this structure is only stable in the presence of water, i.e. in a methyl amine-carbon dioxide-water ice. Notably, in the vibrational frequency calculations on the methylcarbamic acid zwitterion and two water molecules we find the carbon dioxide asymmetric stretch is drastically red shifted by 435 cm(-1) to 1989 cm(-1) and the carbon dioxide symmetric stretch becomes strongly infrared active. We discuss how the methylcarbamic acid zwitterion CH(3)NH(2)(+)CO(2)(-) might be experimentally and astronomically identified by its asymmetric CO(2) stretching mode using infrared spectroscopy.     

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.     

DFT Calculation of Glycine with Methanols Clusters

Density functional theory （DFT） calculations are reported for the structures of neutral and zwitterionic glycine-（CHaOH）n where n=1-6. Initial geometries of the clusters of neutral and zwitterionic glycine with 1-6 methanol molecules are fully optimized at B3LYP/6-31＋G^＊ level of theory. The lowest energy configurations are located and their hydrogen bond structures are analyzed. Theoretical prediction reveals that the methanols prefer to locate near the carboxylic acid group for the small clusters （n_〈3） with the neutral form while the configurations with the methanols bridging the acid and the amino group are favorite in the zwitterionic form clusters. When the number of the methanol molecules in the clusters reaches five and six, the two forms tend to be isoenergetic.     

Monte carlo simulation of water solvent with biomolecules. Glycine and the corresponding zwitterion

Monte Carlo calculations for clusters consisting of 200 water molecules surrounding glycine in the neutral and zwitterionic forms were carried out at 300 K; all the relevant interaction potentials have been obtained by means of quantum–mechanical calculations. Water–water and amino acid–water energies were calculated, and the zwitterion was found to be strongly favored with respect to the neutral molecule, as expected. A detailed analysis of the energetic results yielded some information on the special extension of the solute-induced perturbation. The structural results were found to be in reasonable agreement with predictions that can be obtained by analyzing isoenergy contour maps, calculated for the two-body amino acid–water potential.     

Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer

The relative stabilities of glycine tautomers involved in the intramolecular proton transfer are investigated computationally by considering glycine-water complexes containing up to five water molecules. The supermolecule results are compared with continuum calculations. Specific solute-solvent interactions and solvent induced changes in the solute wave function are considered using the natural bond orbitals (NBO) method. The stabilization of the zwitterion upon solvation is explained by the changes in the wave functions localized on the forming and breaking bonds as well as by the different interaction energies in the zwitterionic and neutral clusters. Only the neutral species exist in mono- and dihydrated clusters and in the gas phase. In the smaller clusters, zwitterions are mainly stabilized by conformational effects, whereas in larger clusters, in particular when glycine is solvated on both sides of its heavy atom backbone, polarization effects dominate the stability of a given tautomer. Generally, the strength of the solute-solvent interactions is governed by the intermolecular charge transfer interactions. As the solvation progresses, the hypothetical gaseous zwitterion is better solvated than the gaseous neutral, making zwitterion to neutral tautomerization progressively less exothermic for clusters containing up to three water molecules, and endothermic for larger clusters. The neutral isomer does not exist for some solvent arrangements with five water molecules. Only solvent arrangements in which water molecules do not interact with the reactive proton are considered. Hence, the experimentally observed double well potential energy surface may be due to such an interaction or to a different reaction mechanism.     

Microsolvation of glycine: a DFT study

PBE1PBE/6-311+G(d,p) computations exploring the microsolvation of neutral and zwitterionic glycine are reported. A broad configuration search was performed to identify the lowest energy clusters of glycine with one to seven water molecules. The structures of the clusters are analyzed on the basis of the hydrogen-bonding network established between the water molecules and between water and glycine. Neutral glycine is favored when associated with zero to six water molecules, but with seven water molecules the two structures are isoenergetic.     

Clusters of hydrated methane sulfonic acid CH3SO3H.(H2O)n (n = 1-5): a theoretical study

Ab initio and density functional methods have been used to examine the structures and energetics of the hydrated clusters of methane sulfonic acid (MSA), CH3SO3H.(H2O)n (n = 1-5). For small clusters with one or two water molecules, the most stable clusters have strong cyclic hydrogen bonds between the proton of OH group in MSA and the water molecules. With three or more water molecules, the proton transfer from MSA to water becomes possible, forming ion-pair structures between CH3SO3- and H3O+ moieties. For MSA.(H2O)3, the energy difference between the most stable ion pair and neutral structures are less than 1 kJ/mol, thus coexistence of neutral and ion-pair isomers are expected. For larger clusters with four and five water molecules, the ion-pair isomers are more stable (>10 kJ/mol) than the neutral ones; thus, proton transfer takes place. The ion-pair clusters can have direct hydrogen bond between CH3SO3- and H3O+ or indirect one through water molecule. For MSA.(H2O)5, the energy difference between ion pairs with direct and indirect hydrogen bonds are less than 1 kJ/mol; namely, the charge separation and acid ionization is energetically possible. The calculated IR spectra of stable isomers of MSA.(H2O)n clusters clearly demonstrate the significant red shift of OH stretching of MSA and hydrogen-bonded OH stretching of water molecules as the size of cluster increases.     

Ab initio molecular dynamics free-energy study of microhydration effects on the neutral-zwitterion equilibrium of phenylalanine.

The structures and relative energies of the most stable conformers of both naked and microsolvated phenylalanine, Phe.(H(2)O)(n)(n=0-3), are calculated by density functional theory. For selected structures, coordination-constrained ab initio molecular dynamics simulations determine the proton-transfer mechanism connecting neutral and zwitterionic forms of Phe. The associated free-energy profiles are calculated by thermodynamic integration. While no zwitterionic free-energy minimum is found for naked Phe, microsolvation is found to stabilize the zwitterionic form. For cluster sizes n > or = 3, the proton-transfer equilibrium shifts towards the zwitterionic structure for specific proton-transfer pathways. The energetically most favourable interconversion path between the neutral and zwitterionic forms is through a H(2)O bridge with free-energy barriers as low as 14.4 kJ mol(-1) for Phe.(H(2)O)(3). The free energy required for breaking a carboxylic OH bond involved in intramolecular hydrogen bonding is typically lower than in the water-assisted case. However, the resulting zwitterion turns out to be unstable with respect to the backward proton-transfer reaction.     

One water molecule stabilizes the cationized arginine zwitterion

Singly hydrated clusters of lithiated arginine, sodiated arginine, and lithiated arginine methyl ester are investigated using infrared action spectroscopy and computational chemistry. Whereas unsolvated lithiated arginine is nonzwitterionic, these results provide compelling evidence that attachment of a single water molecule to this ion makes the zwitterionic form of arginine, in which the side chain is protonated, more stable. The experimental spectra of lithiated and sodiated arginine with one water molecule are very similar and contain spectral signatures for protonated side chains, whereas those of lithiated arginine and singly hydrated lithiated arginine methyl ester are different and contain spectral signatures for neutral side chains. Calculations at the B3LYP/6-31++G** level of theory indicate that solvating lithiated arginine with a single water molecule preferentially stabilizes the zwitterionic forms of this ion by 25-32 kJ/mol and two essentially isoenergetic zwitterionic structure are most stable. In these structures, the metal ion either coordinates with the N-terminal amino group and an oxygen atom of the carboxylate group (NO coordinated) or with both oxygen atoms of the carboxylate group (OO coordinated). In contrast, the OO-coordinated zwitterionic structure of sodiated arginine, both with and without a water molecule, is clearly lowest in energy for both ions. Hydration of the metal ion in these clusters weakens the interactions between the metal ion and the amino acid, whereas hydrogen-bond strengths are largely unaffected. Thus, hydration preferentially stabilizes the zwitterionic structures, all of which contain strong hydrogen bonds. Metal ion size strongly affects the relative propensity for these ions to form NO or OO coordinated structures and results in different zwitterionic structures for lithiated and sodiated arginine clusters containing one water molecule.     

Structures of cationized proline analogues: evidence for the zwitterionic form

The structures of lithiated and sodiated alpha-methyl-proline (alpha-Me-Pro) and structural isomers, both with and without a water molecule, are investigated using blackbody infrared radiative dissociation (BIRD) and density functional theory. From the BIRD kinetic data measured as a function of temperature, combined with master equation modeling of these data, threshold dissociation energies for the loss of a water molecule from these clusters are obtained. These energies are 77.5 +/- 0.5 and 53 +/- 1 kJ/mol for lithiated and sodiated alpha-Me-Pro, respectively. For the nonzwitterionic isomer, proline methyl ester, these values are 3.0-4.5 kJ/mol higher. These results provide compelling experimental evidence that alpha-Me-Pro is zwitterionic in these clusters. Theory at the temperature corrected B3LYP/6-311++G**//B3LYP/6-31++G** level indicates that the salt-bridge or zwitterionic forms of lithiated and sodiated alpha-Me-Pro are between 17 and 23 kJ/mol lower in energy than the nonzwitterionic or charge-solvated forms and that attachment of a single water molecule does not significantly change the structure or the relative energies of these clusters. The proton affinity of proline is 8 kJ/mol higher than that of alpha-Me-Pro, indicating that lithiated and sodiated singly hydrated proline should also be zwitterionic.     

Conformational search for zwitterionic leucine and hydrated conformers of both the canonical and zwitterionic leucine using the DFT-CPCM model

The stable conformations for zwitterionic leucine have been searched for in solution as well as in gas phase. A total of 54 trial structures were generated by considering possible combinations of single bond rotamers. It is observed that zwitterions are not stable in gas phase. In order to investigate the zwitterions of leucine in solution, the calculations for all trial structures of zwitterions were performed initially at the PM3 level and 14 the lowest energy structures were reoptimized at the B3LYP/6-311G(d) level using the CPCM model. Seven of these conformers of zwitterionic leucine were found to be stable in solution. The five most stable conformers were then reoptimized at the B3LYP/6-311++G(d, p) level. The energy ordering of the canonical leucine(neutral) conformers were also considered on the basis of single point energy calculations at the B3LYP/6-311++G(d, p) level using the CPCM model. The chemical hardness, chemical potential, vertical ionization energy and vertical electron affinity were calculated for a few of the most stable canonical leucine and its zwitterions in solution. The effects of explicit addition of water molecules (microsolvation) on the structure and the energy of both canonical and zwitterionic conformers of leucine were investigated. It is noted that in gas phase, the singly and doubly hydrated canonical (neutral) forms are more stable than their zwitterionic counterparts. The solvated zwitterions and canonical structures of leucine were further investigated using the discrete/SCRF model with zero, one and two water molecules. In solution, the continuum solvent model shows that the bare zwitterionic form is more stable than the bare canonical form by 1.6 kcal/mol. This energy separation is increased to 3.8 and 4.8 kcal/mol with inclusion of one and two water molecules, respectively. The optimized structural parameters for the most stable zwitterionic leucine with zero, one and two water molecules in solution were compared with those reported for l-leucine crystal, which shows a close agreement between the optimized geometrical parameters of the zwitterionic leucine with two water molecules in solution with the experimental geometrical parameters for l-leucine crystal. It is also observed that when the structures of zwitterions with one and two explicit water molecules are optimized in solution, the geometrical parameters and their relative energies are found to be appreciably modified. We have also calculated the vibrational spectra of the most stable solvated zwitterionic leucine as well as for the most stable structure of zwitterionic leucine with one and two water molecules in solution.     

Incremental solvation of nonionized and zwitterionic glycine

Microsolvation and combined microsolvation-continuum approaches are employed in order to examine the structures and relative energies of nonionized (N) and zwitterionic (Z) glycine clusters. Bridging structures are predicted to be the global minima after 3-5 discrete water molecules are included in the calculations. Calculations incorporating electron correlation stabilize the zwitterionic structures by about 7-9 kcal/mol relative to the N structures regardless of the number of discrete water molecules considered. Continuum calculations stabilize the Z structures relative to N structures; this effect decreases as the number of discrete water molecules is increased. Eight water molecules do not appear to fully solvate glycine.     

二水合甘氨酸两性离子复合体的结构和性能的理论研究

采用理论计算方法B3LYP, 在6-31++G**基组水平研究使甘氨酸质子化所需的最少水分子数目, 然后讨论水合两性离子复合体的结构和性能, 进而计算了二水合甘氨酸中性分子复合体(2W-GN)到二水合甘氨酸两性离子复合体(2W-GZ)的过渡态, 得到如下结论: (1)两个水分子可以使甘氨酸质子化, 能够形成稳定的二水合两性离子复合体. (2)甘氨酸与水分子之间通过氢键相互作用, 结合能较大, 复合体稳定; 在二水合甘氨酸复合体中, 水合甘氨酸中性分子比水合甘氨酸两性离子稳定. (3)由2W-GN到2W-GZ过程的反应活化能和氢键键能相近.     

Computer simulation of amino acid sorption on carbon nanotubes

A computer simulation of complexes of (6,6) open carbon nanotubes (CNTs) with neutral molecules, zwitterions and glycine, alanine, and phenylalanine amino acid anions is performed. In starting structures amino acids are arranged in three types: on the external side face, the open end, and inside CNT. The structure is optimized within the density functional theory with regard to the GD3 dispersion correction with and without taking into account solvation effects. It is found that the greatest CNT–amino acid interaction occurs in the neutral aqueous medium at dissociative chemisorption of the zwitterion (adsorption energy 80-90 kcal/mol) and in the basic medium at anion chemisorption (energy ~48-50 kcal/mol) on the open CNT end.     

Infrared photodissociation spectroscopy of electrosprayed ions in a Fourier transform mass spectrometer

Previous gas-phase methods for infrared photodissociation spectroscopy (IRPD) require sample volatility. Our method instead uses electrospray ionization to introduce even large nonvolatile molecules into a Fourier transform mass spectrometer, where extended (>15 s) ion storage makes possible high sensitivity spectral measurements with an OPO laser over a range of 3050-3800 cm(-1). The spectra of 22 gaseous proton-bound amino acid complexes are generally correlated with the H-stretching frequencies established for O-H and N-H functional groups in solution. For theoretical structure predictions of the Gly2H+ and N-acylated Asp2H+ dimers, IRPD spectra clearly differentiate between the predicted lowest energy conformers. In contrast to solution, in the gas phase the glycine zwitterion is approximately 20 kcal/mol less stable than the neutral; however, glycine is clearly zwitterionic in the gaseous GlyLysH+ dimer. The level of theory is inadequate for the larger Lys2H+ dimer, as all low energy predicted structures have free carboxyl O-H groups, in contrast to the IR spectrum. IRPD appears to be a promising new technique for providing unique information on a broad range of biomolecular and other gaseous ions, especially on noncovalent bonding involving O-H and N-H groups.     

Modelling zwitterions in solution: 3-fluoro-γ-aminobutyric acid (3F-GABA)

The conformations and relative stabilities of folded and extended 3-fluoro-γ-aminobutyric acid (3F-GABA) conformers were studied using explicit solvation models. Geometry optimisations in the gas phase with one or two explicit water molecules favour folded and neutral structures containing intramolecular NH···O-C hydrogen bonds. With three or five explicit water molecules zwitterionic minima are obtained, with folded structures being preferred over extended conformers. The stability of folded versus extended zwitterionic conformers increases on going from a PCM continuum solvation model to the microsolvated complexes, though extended structures become less disfavoured with the inclusion of more water molecules. Full explicit solvation was studied with a hybrid quantum-mechanical/molecular-mechanical (QM/MM) scheme and molecular dynamics simulations, including more than 6000 TIP3P water molecules. According to free energies obtained from thermodynamic integration at the PM3/MM level and corrected for B3LYP/MM total energies, the fully extended conformer is more stable than folded ones by about -4.5 kJ mol(-1). B3LYP-computed (3)J(F,H) NMR spin-spin coupling constants, averaged over PM3/MM-MD trajectories, agree best with experiment for this fully extended form, in accordance with the original NMR analysis. The seeming discrepancy between static PCM calculations and experiment noted previously is now resolved. That the inexpensive semiempirical PM3 method performs so well for this archetypical zwitterion is encouraging for further QM/MM studies of biomolecular systems.     

Theoretical Studies on the Hydrogen Bond Transfer and Proton Transfer between Anamorphoses of the Dihydrated Glycine Complex

The conversion between anamorphoses of the dihydrated glycine complex was studied by means of B3LYP/6-31++G**. It was found that proton transfer was accompanied by hydrogen bond transfer in the process of conversion between different kinds of anamorphoses. With proton transfer, the electrostatic action was notably increased and the hydrogen-bonding action was evidently strengthened when the dihydrated neutral glycine complex converts into dihydrated zwitterionic glycine complex. The activation energy required for hydrogen bond transfer between dihydrated neutral glycine complexes is very low (6.32 kJ·mol-1); however, the hydrogen bond transfer between dihydrated zwitterionic glycine complexes is rather difficult with the required activation energy of 13.52 kJ·mol-1 due to the relatively strong electrostatic action. The activation energy required by proton transfer is at least 27.33 kJ·mol-1, higher than that needed for hydrogen bond transfer. The activation energy for either hydrogen bond transfer or proton transfer is in the bond-energy scope of medium-strong hydrogen bond, so the four kinds of anamorphoses of the dihydrated glycine complex could convert mutually.     

A novel quantum mechanical/molecular mechanical approach to the free energy calculation for isomerization of glycine in aqueous solution

The free energy change associated with the isomerization reaction of glycine in water solution has been studied by a hybrid quantum mechanical/molecular mechanical (QM/MM) approach combined with the theory of energy representation (QM/MM-ER) recently developed. The solvation free energies for both neutral and zwitterionic form of glycine have been determined by means of the QM/MM-ER simulation. The contributions of the electronic polarization and the fluctuation of the QM solute to the solvation free energy have been investigated. It has been found that the contribution of the density fluctuation of the zwitterionic solute is estimated as -4.2 kcal/mol in the total solvation free energy of -46.1 kcal/mol, while that of the neutral form is computed as -3.0 kcal/mol in the solvation free energy of -15.6 kcal/mol. The resultant free energy change associated with the isomerization of glycine in water has been obtained as -7.8 kcal/mol, in excellent agreement with the experimental data of -7.3 or -7.7 kcal/mol, implying the accuracy of the QM/MM-ER approach. The results have also been compared with those computed by other methodologies such as the polarizable continuum model and the classical molecular simulation. The efficiency and advantage of the QM/MM-ER method has been discussed.     

5水合甘氨酸复合体的结构和性能的理论研究

为了探讨“几个水分子导致甘氨酸两性离子复合体与其中性分子复合体等能”, 采用mp2/6-31＋＋g**//b3lyp/6- 31＋＋g**方法研究了甘氨酸水化的微观机理, 发现答案是5个水分子, 并证实了实验结果. 最稳定的5水合甘氨酸两性离子复合体具有双链结构, 与最稳定的5水合甘氨酸中性分子复合体能量接近(仅相差2.26 kJ/mol), 能够共存; 中性复合体和两性复合体之间可以通过直接质子迁移和桥助质子迁移等两种途径相互转化, 双链结构的甘氨酸复合体中质子迁移的能垒较低甚至无垒, 能够自发进行.