Structures of dense glycine and alanine adlayers on chiral Cu(3,1,17) surfaces

Density Functional Theory calculations have been used to predict the structures of dense glycine and alanine adlayers on Cu(3,1,17)(S). Facets of this chiral Cu surface result from adsorbate-induced surface reconstruction when glycine or alanine are adsorbed and annealed on Cu(100). We have calculated the surface energy changes associated with this surface reconstruction. Our results allow the enantiospecificity of this reconstruction following adsorption of enantiopure or racemic alanine on Cu(100) to be discussed. The overall stability of glycine and alanine adlayers on Cu(3,1,17)(S) arises from an interplay between the formation of chemical bonds with the Cu surface, deformations in the adsorbed molecules during adsorption, and intermolecular hydrogen bonds within the adlayer; none of these factors individually dominates.     

Structures of glycine, enantiopure alanine, and racemic alanine adlayers on Cu(110) and Cu(100) surfaces

We have determined the structures of dense adlayers of glycine and alanine on the Cu(110) and Cu(100) surfaces using plane wave density functional theory. These calculations resolve several experimental controversies regarding these structures. Glycine exists on Cu(110) as a single adlayer structure, while on Cu(100) two distinct glycine adlayers coexist. The glycine structures serve as useful starting points for constructing alanine adlayer structures. We considered separately the adsorption of enantiopure alanine and racemic alanine on each surface. Adlayers of enantiopure alanine are found to be closely related to the adlayers observed for glycine. Racemic alanine adlayers on Cu(110) are structurally analogous to those observed for glycine on this surface and adopt a pseudo-racemate ordering. On Cu(100), in contrast to glycine, racemic alanine is found to adopt a single adlayer structure that is an ordered racemate. Spontaneous segregation of molecular enantiomers does not occur in racemic adsorbed mixtures on either surface. Consideration of the orientationally distinct domains that may exist for each adlayer on these surfaces provides important information for the interpretation of the adlayer domain boundaries that are commonly observed in scanning tunneling microscopy images of amino acid adlayers. Examining this set of amino acid adlayers provides useful insight into the range of subtle behaviors that can arise in these and related systems where chiral molecules form ordered adlayers on flat metal surfaces.     

Resorcinarene-based cavitands with chiral amino acid substituents for chiral amine recognition

Resorcinarene-based deep cavitands alanine methyl resorcinarene acid (), alanine undecyl resorcinarene acid () and glycine undecyl resorcinarene acid (), which contain chiral amino acids, have been synthesized. The upper rim of the resorcinarene host is elongated with four identical substituents topped with alanine and glycine groups. The structures of the new resorcinarenes were elucidated by nuclear magnetic resonance (NMR), mass spectrometry (MS) and the sustained off-resonance irradiation collision induced dissociation (SORI-CID) technique in FTICR-MS. These studies revealed that eight water molecules associate to the cavitand, two for each alanine group. The alanine substituent groups are proposed to form a kite-like structure around the resorcinarene scaffold. The binding of , , and with chiral R- and S-methyl benzyl amines was studied by (1)H NMR titration, and compared to that of a binary l-tartaric acid and the monoacid phthalyl alanine (). The results show that these compounds interact with amine guests; however, with four carboxylic acid groups, they bind several amine molecules strongly while the binary l-tartaric acid only binds one amine guest strongly. The simple compound , which contains one carboxylic group, shows weak binding to the amines. The (1)H NMR titration of with primary, secondary, and tertiary chiral amines showed that it can discriminate between these three types of amines and showed chiral discrimination for chiral secondary amines.     

Characterization of enantiospecific chemisorption on chiral Cu surfaces vicinal to Cu(111) and Cu(100) using density functional theory

Surfaces of simple fcc metals such as Cu with nonzero and unequal Miller indices are intrinsically chiral. Density functional theory (DFT) calculations are a useful way to study the enantiospecific adsorption of small chiral molecules on these chiral metal surfaces. We report DFT calculations of seven chiral molecules on several structurally distinct chiral Cu surfaces. These surfaces include two surfaces with (111)-oriented terraces and one with (100)-oriented terraces. Calculations are also described on a surface that was modified to mimic the surface structures that typically appear on real metal surfaces following thermally driven fluctuations in step edges. Our results provide initial information on how variation in the surface structure of intrinsically chiral metal surfaces can affect the enantiospecific adsorption of small molecules on these surfaces.     

Synthesis,characterization, equilibrium studies,and biological activity of complexes involving copper(II), 2-aminomethylthiophenyl-4-bromosalicylaldehyde Schiff base,and selected amino acids

Ternary complexes of copper(II) with 2-aminomethylthiophenyl-4-bromosalicylaldehyde (ATS) and some amino acids have been isolated and characterized by elemental analyses, IR, magnetic moment, molar conductance, UV–vis, mass spectra, and ESR. The proposed general formulas of the prepared complexes are [Cu(ATS)(AA)]·nH₂O (where AA?=?glycine, alanine, and valine). The low molar conductance values suggest the non-electrolytic nature of the complexes. IR spectra show that ATS is coordinated to copper in a bidentate manner through azomethine-N and phenolic-OH. The amino acids also are monobasic bidentate ligands via amino and ionized carboxylate groups. The magnetic and spectral data indicate the square-planar geometry of Cu(II) complexes. The geometry of the Cu(II) complexes has been fully optimized using parameterized PM3 semiempirical method. The Cu–N bond length is longer than that of Cu–O in the isolated complexes. Also, information is obtained from calculations of molecular parameters for all complexes including net dipole moment of the metal complexes, values of binding energy, and lipophilicity value (log P). The antimicrobial activity studies indicate significant inhibitory activity of complex 3 against the selected types of bacteria. The mixed ligand complexes have also been studied in solution state. Protonation constants of ATS and amino acids were determined by potentiometric titration in 50% (v/v) DMSO–water solution at ionic strength of 0.1?M NaCl. ATS has two protonation constants. The binary and ternary complexes of copper(II) involving ATS and some selected amino acids (glycine, alanine, and valine) were examined. Copper(II) forms [Cu(ATS)], [Cu(ATS)₂], [Cu(AA)], [Cu(AA)₂], and [Cu(ATS)(AA)] complexes. The ternary complexes are formed in a simultaneous mechanism.     

Cation-π effects in the complexation of Na+ and K+ with Phe, Tyr, and Trp in the gas phase

Na⁺ and K⁺ gas-phase affinities of the three aromatic amino acids Phe, Tyr, and Trp were measured by the kinetic method. Na⁺ binds these amino acids much more strongly than K⁺, and for both metal ions the binding strength was found to follow the order Phe ≤ Tyr < Trp. Quantum chemical calculations by density functional theory (DFT) gave the same qualitative ordering, but suggested a somewhat larger Phe/Trp increment. These results are in acceptable agreement with predictions based on the binding of Na⁺ and K⁺ to the side chain model molecules benzene, phenol, and indole, and are also in reasonable agreement with the predictions from purely electrostatic calculations of the side-chain binding effects. The binding energies were compared with those to the aliphatic amino acids glycine and alanine. Binding to the aromatic amino acids was found to be stronger both experimentally and computationally, but the DFT calculations indicate substantially larger increments relative to alanine than shown by the experiments. Possible reasons for this difference are discussed. The metal ion binding energies show the same trends as the proton affinities.     

Formation and Fragmentation of Protonated Molecules after Ionization of Amino Acid and Lactic Acid Clusters by Collision with Ions in the Gas Phase

Collisions between O³⁺ ions and neutral clusters of amino acids (alanine, valine and glycine) as well as lactic acid are performed in the gas phase, in order to investigate the effect of ionizing radiation on these biologically relevant molecular systems. All monomers and dimers are found to be predominantly protonated, and ab initio quantum–chemical calculations on model systems indicate that for amino acids, this is due to proton transfer within the clusters after ionization. For lactic acid, which has a lower proton affinity than amino acids, a significant non‐negligible amount of the radical cation monomer is observed. New fragment‐ion channels observed from clusters, as opposed to isolated molecules, are assigned to the statistical dissociation of protonated molecules formed upon ionization of the clusters. These new dissociation channels exhibit strong delayed fragmentation on the microsecond time scale, especially after multiple ionization.     

Supramolecular assembly of strongly chemisorbed size- and shape-defined chiral clusters: S- and R-alanine on Cu(110)

The bonding and self-assembly of a chirally organized monolayer of alanine on the Cu(110) surface has been investigated using reflection-absorption infrared spectroscopy, low-energy electron diffraction (LEED), and scanning tunneling microscopy (STM). This multitechnique approach has enabled an in-depth understanding of the hierarchy of chirality transfer: from a single adsorbed molecule, to size-defined chiral clusters, and then to an overall chiral assembly. The data have indicated that the alanine is in its anionic form, bound to the copper surface through the oxygens of the ionized carboxylate group and the nitrogen of the neutral amino group. Importantly, the methyl group is held away from the surface, resulting in direct chirality transfer into the footprint of the adsorbed alanine molecules, with the local adsorption motif for S-alanine being the mirror image of that created for R-alanine. STM has shown that S-alanine molecules self-organize to form size-defined chiral clusters of six or eight molecules at the surface, interspersed with chiral channels of bare metal. Together, these clusters and channels further self-assemble into a chiral array with one unique chiral domain sustained across the entire surface. A similar chiral assembly, but with the mirror organization, has been observed for R-alanine. Structural models for the individual clusters are proposed, and in conjunction with LEED data, overall models for these chiral phases of both S- and R-alanine have been constructed. Overall, this adsorption system has been found to be both strongly chemisorbed and capable of extensive intermolecular H-bonding, causing stresses that lead not only to the chiral self-organization of molecules but also to a specific self-organization of the empty chiral channels and spaces that intersperse the structure which, in turn, chirally assemble across macroscopic length scales to give a surface with global organizational chirality.     

Silicon amino acids

The existence and gas phase stability of silicon analogues of three natural amino acids (i.e., silicon glycine, silicon alanine, and silicon valine) belonging to the novel class of compounds termed silicon amino acids (SiAA) are investigated theoretically on the basis of ab initio QCISD/aug‐cc‐pVTZ and MP2/aug‐cc‐pVTZ calculations. All molecules studied (in their gas phase canonical forms) are structurally comparable to their proteinogenic counterparts (i.e., glycine, l ‐alanine, and l ‐valine) and capable of forming several structural isomers as such. These higher energy isomers are characterized by small relative energies (not exceeding 4 kcal mol⁻¹). The simulated IR spectra of the Si‐Gly, Si‐Ala, and Si‐Val global minima are also presented and discussed.     

Highly enantioselective discrimination of amino acids using copper deposition on a gold electrode modified with homocysteine monolayer

An extremely enhanced enantioselectivity was achieved for the detection of enantiomers of alanine (Ala), leucine (Leu), and 3,4-dihydroxyphenylalanine (DOPA) based on the voltammograms for the deposition of Cu from Cu complexes of the amino acids at an Au electrode modified with a self-assembled monolayer (SAM) of l-homocysteine (Hcy). The enantioselective current density peak for the Cu deposition was found to change with increasing number of potential cycles after the addition of Cu(II), and the highest enantioselectivity was observed immediately after the addition of Cu(II). Besides, enantioselectivity was not observed with proline, whose five-membered ring contains the nitrogen atom of a secondary amino group, while some amino acids with a primary amine group such as Ala, Leu, and DOPA exhibited enantioselectivity. These results suggest that the chiral ligand exchange reaction at the l-Hcy SAM-modified Au electrode, namely, the enantioselective formation of diastereomeric complexes of Cu(II) with target enantiomers and l-Hcy self-assembled on the Au electrode, plays an important role in the chiral discrimination based on the Cu deposition.     

Probing enantioselectivity on chirally modified Cu(110), Cu(100), and Cu(111) surfaces

Temperature programmed desorption methods have been used to probe the enantioselectivity of achiral Cu(100), Cu(110), and Cu(111) single crystal surfaces modified by chiral organic molecules including amino acids, alcohols, alkoxides, and amino-alcohols. The following combinations of chiral probes and chiral modifiers on Cu surfaces were included in this study: propylene oxide (PO) on L-alanine modified Cu(110), PO on L-alaninol modified Cu(111), PO on 2-butanol modified Cu(111), PO on 2-butoxide modified Cu(100), PO on 2-butoxide modified Cu(111), R-3-methylcyclohexanone (R-3-MCHO) on 2-butoxide modified Cu(100), and R-3-MCHO on 2-butoxide modified Cu(111). In contrast with the fact that these and other chiral probe/modifier systems have exhibited enantioselectivity on Pd(111) and Pt(111) surfaces, none of these probe/modifier/Cu systems exhibit enantioselectivity at either low or high modifier coverages. The nature of the underlying substrate plays a significant role in the mechanism of hydrogen-bonding interactions and could be critical to observing enantioselectivity. While hydrogen-bonding interactions between modifier and probe molecule are believed to induce enantioselectivity on Pd surfaces (Gao, F.; Wang, Y.; Burkholder, L.; Tysoe, W. T. J. Am. Chem. Soc. 2007, 129, 15240-15249), such critical interactions may be missing on Cu surfaces where hydrogen-bonding interactions are believed to occur between adjacent modifier molecules, enabling them to form clusters or islands.     

Chemical speciation of adsorbed glycine on metal surfaces

Experimental studies have reported that glycine is adsorbed on the Cu(110) and Cu(100) surfaces in its deprotonated form at room temperature, but in its zwitterionic form on Pd(111) and Pt(111). In contrast, recent density functional theory (DFT) calculations indicated that the deprotonated molecules are thermodynamically favored on Cu(110), Cu(100), and Pd(111). To explore the source of this disagreement, we have tested three possible hypotheses. Using DFT calculations, we first show that the kinetic barrier for the deprotonation reaction of glycine on Pd(111) is larger than on Cu(110) or Cu(100). We then report that the presence of excess hydrogen would have little influence on the experimentally observed results, especially for Pd(111). Lastly, we perform Monte Carlo simulations to demonstrate that the aggregates of zwitterionic species on Pt(111) are energetically preferred to those of neutral species. Our results strongly suggest that the formation of aggregates with relatively large numbers of adsorbed molecules is favored under experimentally relevant conditions and that the adsorbate-adsorbate interactions in these aggregates stabilize the zwitterionic species.     

Theoretical study of the electronic gas-phase spectrum of glycine, alanine, and related amines and carboxylic acids

A theoretical study on the origin of the common electronic excitations in amino acids is presented, focusing on the excited states of glycine, alanine and the related substructures formic acid, acetic acid, propionic acid, ammonia, methylamine, and ethylamine. Special attention is given to the valence excitation from the nonbonding lone-pair on the carboxylic oxygen atom to the antibonding pi-orbital (n(O) --> pi*(CO)) and the first Rydberg excitation from the nonbonding lone-pair on the nitrogen atom (n(N) --> 3s). From extensive calculations on formic acid and methylamine, different basis sets and electron correlation treatments are benchmarked using a hierarchy of coupled cluster (CC) methods, consisting of CCS, CC2, CCSD, CCSDR(3), and CC3, in combination with augmented correlation consistent basis sets. The dependence of the excitation energies on the size of the backbone structure in the two groups of molecules is investigated, and 0-0 transition energies for the n(O) --> pi*(CO) and n(N) --> 3s transitions are calculated for the smallest molecules. Excellent agreement with experimental values is found where secure experimental assignments are available. A few outstanding problems in the experimental assignments found in the literature are described for both the carboxylic acids and the amines. Final predictions for vertical excitation energies are given for all molecules, including glycine and alanine where no gas-phase experimental results are available. Finally, calculations on protonated amino acids are presented showing an isolation of the n(O) --> pi*(CO) from higher lying states by as much as 1.9 eV for alanine.     

2D separations on a 1D chip: gradient elution moving boundary electrophoresis-chiral capillary zone electrophoresis

A new method is described for two-dimensional (2D) separations using a microfluidic chip normally employed for single dimension electrophoresis. The method employs a combination of gradient elution moving boundary electrophoresis (GEMBE) and chiral capillary zone electrophoresis (CZE). The simplicity of the first dimension GEMBE method enables its implementation in the injection channel of a conventional electrophoresis chip, simplifying the design and operation of the device. The method was used for high resolution 2D chiral separations of a mixture of amino acids considered as possible signatures of extant or extinct life for solar system exploration. The enantiomers of aspartic acid, glutamic acid, serine, alanine, and valine were all resolved as well as glycine (achiral) and several unidentified impurities, giving an estimated peak capacity of 35 for the region between valine and glycine. The results highlight the need for high peak capacity separations for chiral amino acid analysis if accurate enantiomeric ratios are to be determined.     

Design of radical-resistant amino acid residues: a combined theoretical and experimental investigation

Ab initio calculations have been used to design radical-resistant amino acid residues. Optimized structures of free and protected amino acids and their corresponding alpha-carbon-centered radicals were determined with B3-LYP/6-31G(d). Single-point RMP2/6-31G(d) calculations on these structures were then used to obtain radical stabilization energies, to examine the effect of steric repulsion between the side chains and amide carbonyl groups on the stability of alpha-carbon-centered peptide radicals. Relative to glycine, the destabilization for alanine and valine residues was found to be approximately 9 and 18 kJ mol(-1), respectively, which correlates with the reactivity of analogous amino acid residues in peptides toward hydrogen atom abstraction in conventional free radical reactions. To design amino acid residues that would resist radical reactions, strategies by which the steric effects could be magnified were considered. This resulted in the identification of tert-leucine and 3,3,3-trifluoroalanine as suitable molecules. With these amino acid residues, the destabilization of the alpha-carbon-centered radicals relative to that of glycine is increased substantially to approximately 36 and 41 kJ mol(-1), respectively. The theoretical predictions have been supported by experimental observations: a tert-leucine derivative was shown to be very slow to react with N-bromosuccinimide, while the corresponding trifluoroalanine derivative was found to be inert.     

Computational (DFT) and Experimental (NMR) Study of the Chelation of an Iridium Hyperpolarization Transfer Catalyst by Amino Acids

Non-hydrogenative Para-Hydrogen Induced Hyperpolarization (nhPHIP) is a Nuclear Magnetic Resonance (NMR) hyperpolarization technique which has experimentally been used to analyze complex biological samples containing amino acids using the Ir-IMes hyperpolarization transfer catalyst. A computational study based on Density Function Theory (DFT) was performed on all relevant stereoisomers of [Ir(H)₂(IMes)(AA)(Py)] (with AA=glycine, alanine, valine; Py=pyridine), for which R/S chirality and orientation of the amino acid chelation (C/A) were considered. A total of 30 structures were calculated comprising of 6 stereoisomers for achiral glycine, and 12 stereoisomers for each of the chiral amino acids. The abundances derived from the DFT energies confirmed the trends observed in thermal (non-hyperpolarized) NMR experiments. Additionally, theoretical calculations of electronic (Wiberg bond indices, Natural Bond Orders, Frontier Orbital Analysis), bond dissociation energies, transition states, and activation energies related to interconversion between binding modes, and steric factors (Solid angle) were performed to provide detailed explanations for NMR experimental observations.     

Racemic versus enantiopure alanine on Cu(110): an experimental study

The adsorption of racemic alanine on the Cu(110) surface has been compared to that of enantiopure alanine using low-energy electron diffraction (LEED), reflection absorption infrared spectroscopy (RAIRS), and scanning tunneling microscopy (STM). No evidence of chiral resolution at the surface was observed for the racemic system, indicating that the formation of separate enantiopure areas is not preferred. Also, in contrast to the enantiopure system, no chirally organized phase was observed for the racemic system. LEED shows that both systems display a common (3 x 2) phase at high coverage. However, the pathway and kinetic barriers to this phase differ markedly for the racemic and the enantiopure systems, with the racemic (3 x 2) appearing at a temperature that is more than 100 K below that required for the enantiopure system. In addition, we report intriguing complexities for the (3 x 2) LEED structure that is ubiquitous in amino acid/Cu(110) systems. First, a common (3 x 2) pattern with a zigzag distortion can be associated with both the racemic and enantiopure systems. For the racemic system, the coverage can be increased further to give a "true" (3 x 2) LEED pattern, which is a transformation that is impossible to enact for the enantiopure system. Most importantly, STM images of the "distorted" and "true" (3 x 2) structures created in the racemic system show subtle differences with neither arrangement being fully periodic over distances greater than a few molecules. Thus, the (3 x 2) phase appears to be more complicated than at first indicated and will require more complex models for a full interpretation.     

Chiral close-packing of achiral star-shaped molecules on solid surfaces

From the interplay of scanning tunneling microscopy and theoretical calculations, we study the chiral self-assembly of achiral HtB-HBC molecules upon adsorption on the Cu(110) surface. We find that chirality is expressed at two different levels: a +/-5 degrees rotation of the molecular axis with respect to the close-packed direction of the Cu(110) substrate and a chiral close-packed arrangement expected for star-shaped molecules in 2D. Out of the four possible chiral expressions, only two are found to exist due the effect of van der Waals (vdW) interactions forcing the molecules to simultaneously adjust to the atomic template of the substrate geometry and self-assemble in a close-packed geometry.     

A step toward the wet surface chemistry of glycine and alanine on Cu{110}: destabilization and decomposition in the presence of near-ambient water vapor

The coadsorption of water with organic molecules under near-ambient pressure and temperature conditions opens up new reaction pathways on model catalyst surfaces that are not accessible in conventional ultrahigh-vacuum surface-science experiments. The surface chemistry of glycine and alanine at the water-exposed Cu{110} interface was studied in situ using ambient-pressure photoemission and X-ray absorption spectroscopy techniques. At water pressures above 10(-5) Torr a significant pressure-dependent decrease in the temperature for dissociative desorption was observed for both amino acids, accompanied by the appearance of a new CN intermediate, which is not observed for lower pressures. The most likely reaction mechanisms involve dehydrogenation induced by O and/or OH surface species resulting from the dissociative adsorption of water. The linear relationship between the inverse decomposition temperature and the logarithm of water pressure enables determination of the activation energy for the surface reaction, between 213 and 232 kJ/mol, and a prediction of the decomposition temperature at the solid-liquid interface by extrapolating toward the equilibrium vapor pressure. Such experiments near the equilibrium vapor pressure provide important information about elementary surface processes at the solid-liquid interface, which can be retrieved neither under ultrahigh vacuum conditions nor from interfaces immersed in a solution.     

Gas-Phase Binding of Noncovalent Complexes Between α-cyclodextrin and Amino Acids Investigated by Mass Spectrometry

Noncovalent complexes between cyclodextrins and small molecules have been extensively studied recently because of their widespread application in the pharmaceutical industry for chiral and molecular recognition. To date, gas phase noncovalent binding affinities between α-cyclodextrin and amino acids have not been widely investigated. In this study, gas-phase binding of noncovalent complexes between α-CD and amino acids was investigated by electrospray ionization mass spectrometry (ESI-MS), demonstrating the formation of 1:1 stoichiometric noncovalent complexes. The binding of the complexes were further confirmed by collision-induced dissociation by tandem mass spectrometry. Mass spectrometric titrations between α-cyclodextrin and phenylalanine, glutamic acid, and arginine were performed to provide binding constants (lgK_a) as references for competitive ESI-MS. Calibration curves for the complexes of α-cyclodextrin with phenylalanine, glutamic acid, and arginine were plotted. Through competitive ESI-MS, the lgK_a for the complexes of α-CD with aspartic acid, lysine, proline, glycine, alanine, asparagine, cystine, glutamine, histidine, leucine, isoleucine, methionine, serine, threonine, and valine were measured directly. By comparison, it is seen that the measured binding constants for the complexes of α-cyclodextrin with basic amino acids such as arginine and lysine are lower than those for most complexes of neutral amino acids. The chiral selectivity of α-cyclodextrin for L- and D-isomers of methionine, threonine, asparagine, and phenylalanine determined by ESI-MS revealed its application as a chiral selector.