Infrared Spectral, Structural, and Conformational Studies of Zwitterionic l-Tryptophan

Exploration of electronic and vibrational properties of sulfanilic acid through periodic and non-periodic DFT calculations

CONTEXT

The electronic, discrete water solvation, and vibrational properties of zwitterionic sulfanilic acid were thoroughly investigated using periodic and non-periodic DFT approaches. The periodic-DFT results, obtained by employing the PBE-TS functional (Perdew-Burke-Ernzerhof (PBE) functional with the Tkatchenko and Scheffler (TS) dispersion correction) were first presented in order to analyze the band structures of the studied crystal. An attentive reading of the predicted band structures has shown three lowest gap energies calculated at 4.23, 4.24, and 4.29 eV arising from the Γ→Γ, Γ→Z, and Γ→S transitions, respectively. Then, non-periodic calculations were carried out, at the B3LYP-D3 level of theory (B3LYP functional with the D3 Grimme dispersion correction) in order to optimize the sulfanilic acid-(H2O)10 complex. Starting from the optimized structure, non-covalent interaction calculations were performed and the H-bonding, van der Waals, and steric effect interactions were identified. Finally, the PBE-TS calculations were strengthened by conducting anharmonic B3LYP-D3 calculations in order to achieve a complete decryption of the experimental IR spectrum of sulfanilic acid. The spectral analysis is not limited only to the interpretation of both the NH/CH stretching and fingerprint regions but also extended to the 1800-2600 cm-1 region, which is characterized by a strong anharmonic effect. In the latter wavenumber region, the large experimental IR band centered at 1937 cm-1 is reproduced theoretically employing the anharmonic B3LYP-D3 calculations. The similarity of this band with those usually considered as a fingerprint of zwitterionic amino acids is observed, and its origin is elucidated theoretically. In the vibrational spectroscopy field, the calculations presented in this study are probably the most appropriate for achieving vast analysis and accurate assignments of vibrational spectra of hydrogen bonding compounds recorded in the solid state.

METHOD

The periodic and non-periodic calculations were conducted within the Density Functional Theory (DFT) using the Generalized Gradient Approximation (GGA) at the PBE-TS level of theory and B3LYP-D3 functional with the 6-311++G(d,p) basis set, respectively. The PBE-TS and B3LYP-D3/6-311++G(d,p) calculations were performed using the CASTEP and Gaussian 09 programs, respectively. In addition, The non-covalent interactions were calculated by the Multiwfn 3.8 software. The obtained results for different calculations were visualized by employing the visualization tools in Materials Studio, GaussView, VMD, and Gnuplot programs.

Non-salt based co-amorphous formulation produced by freeze-drying

Amino acids-based co-amorphous system (CAM) has shown to be a promising approach to overcome the dissolution challenge of biopharmaceutics classification system class II drugs. To date, most CAM formulations are based on salt formation at a 1:1 M ratio and are prepared by mechanical activation. However, its use in medicinal products is still limited due to the lack of in-depth understanding of non-ionic based molecular interactions. There are also limited studies on the effect of drug-to-co-former ratio, the development of more scalable, less aggressive, manufacturing processes such as freeze drying and its dissolution benefits. This work aims to investigate the effect of the ratio of tryptophan (a model non-ionic amino acid) to indomethacin (a model drug) on a non-salt-based CAM prepared via freeze-drying with the tert-butyl alcohol-water cosolvent system. The CAM material was systemically characterized at various stages of the freeze-drying process using DSC, UV-Vis, FT-IR, NMR, TGA and XRPD. Dissolution performance and physical stability upon storage were also investigated. Freeze-drying using the cosolvent system has been successfully shown to produce CAMs. The molecular interactions involving H-bonding, H/π and π-π between compounds have been confirmed by FT-IR and NMR. The drug release rate for formulations with a 1.5:1 drug: amino acid molar ratio (or 1:0.42 wt ratio) or below is found to be significantly improved compared to the pure crystalline drug. Furthermore, formulation with a 2.3:1 drug:amino acid molar ratio (or 1:0.25 wt ratio) or below have shown to be physically stable for at least 9 months when stored at dry condition (5% relative humidity, 25 °C) compared to the pure amorphous indomethacin. We have demonstrated the potential of freeze-drying using tert-butyl alcohol-water cosolvent system to produce an optimal non-salt-based class II drug-amino acid CAM.

Amorphous Solid Forms of Ranolazine and Tryptophan and Their Relaxation to Metastable Polymorphs

Different methods were explored for the amorphization of ranolazine, a sparingly soluble anti-anginal drug, such as mechanochemistry, quench-cooling, and solvent evaporation from solutions. Amorphous phases, with Tg values lower than room temperature, were obtained by cryo-milling and quench-cooling. New forms of ranolazine, named II and III, were identified from the relaxation of the ranolazine amorphous phase produced by cryo-milling, which takes place within several hours after grinding. At room temperature, these metastable polymorphs relax to the lower energy polymorph I, whose crystal structure was solved in this work for the first time. A binary co-amorphous mixture of ranolazine and tryptophan was produced, with three important advantages: higher glass transition temperature, increased kinetic stability preventing relaxation of the amorphous to crystalline phases for at least two months, and improved aqueous solubility. Concomitantly, the thermal behavior of amorphous tryptophan obtained by cryo-milling was studied by DSC. Depending on experimental conditions, it was possible to observe relaxation directly to the lower energy form or by an intermediate metastable crystalline phase and the serendipitous production of the neutral form of this amino acid in the pure solid phase.

New ternary Fe(III)-8-hydroxyquinoline-reduced Schiff base complexes as selective anticancer drug candidates

Due to the growing prevalence of cancer diseases, new therapeutic options are urgently needed, and drugs based on metal ions other than platinum are alternatives with exciting possibilities. We report the synthesis, characterization and biological effect of mixed-ligand Fe(III)-aminophenolate complexes derived from salicylaldehyde and L-tryptophan with quinoline derivatives as co-ligands, namely 8-hydroxyquinoline (8HQ), [Fe(L)(8HQ)(H₂O)] (1) and its 5-cloro derivative (Cl8HQ), [Fe(L)(Cl8HQ)(H₂O)] (2). The complex bearing the aminophenolate and lacking the quinoline co-ligand, [Fe(L)(Cl)(H₂O)₂] (3), was prepared for comparison. The analytical and spectroscopic characterization revealed that 1 and 2 are octahedral Fe(III) complexes with the aminophenolate acting as a dianionic tridentate ligand and 8HQ co-ligands as bidentate chelates. Spectroscopic techniques and molecular docking studies were used to evaluate the ability of these complexes to bind bovine serum albumin (BSA) and calf thymus DNA. Complex 2 [Fe(L)(Cl8HQ)(H₂O)] was the one showing higher affinity for both biomolecules. Cell viability was assessed in breast, colorectal and bone human cancer cell lines. 1 and 2 were found to be more active than cisplatin in all cell lines tested. A non-tumoral fibroblast line (L929, mouse non-tumoral fibroblasts) was used to evaluate selectivity. The results evidence that 2 shows much higher selectivity than 1 in all cell lines tested, but particularly in bone cancer cells in which selectivity index (SI) values are 8.0 and 18.8 for 1 and 2, respectively.

Fourier-transform infrared spectroscopy of human IgG Fc fragments, which are a promising drug for the treatment of autoimmune diseases

IgG Fc fragments that expose regulatory rheumatoid factor epitopes (regRF epitopes) have emerged as a promising immunosuppressive drug. Immunization of rats with such Fc fragments reduced symptoms of experimental autoimmune diseases. The immunosuppressive effect of Fc fragments is based on stimulating the production of regRF, which kills activated CD4 T lymphocytes. The formation of regRF epitopes on Fc fragments was previously shown to be associated with a reduction in disulfide bonds in the fragments' hinge region. However, the structure of Fc fragments that bear regRF epitopes remained largely unclear. Infrared spectra were compared for lyophilized Fc fragments displaying regRF epitopes and Fc fragments without such epitopes. FTIR spectroscopy found no differences in the amide I, amide II, and amide III bands, indicating that there are no distinctive features in the secondary structure of Fc fragments bearing regRF epitopes. The distinctive feature of Fc fragments bearing regRF epitopes, irrespective of whether the free SH groups in the hinge were preserved or lost after lyophilization, is the presence of a band or a fine structure in the region containing the bending vibrations of the SH groups. Furthermore, the Fc fragments with regRF epitopes differ from those without in that they have a band in the absorption region of aromatic amino acid rings. Taken together, these facts suggest that the appearance of regRF epitopes results from changes in the tertiary structure of the hinge and the domains that occur when the hinge is reduced, and they also indicate that these conformational changes are resistant to subsequent changes in the state of cysteine residues in the hinge. Bands in the regions of aromatic amino acids and the bending vibrations of SH groups are markers of the presence of regRF epitopes on IgG Fc fragments. FTIR spectroscopy can be used to detect these epitopes.

The Effect of the Presence of Amino Acids on the Precipitation of Inorganic Chemical-Garden Membranes: Biomineralization at the Origin of Life

If life developed in hydrothermal vents, it would have been within mineral membranes. The first proto-cells must have evolved to manipulate the mineral membranes that formed their compartments in order to control their metabolism. There must have occurred a biological takeover of the self-assembled mineral structures of the vents, with the incorporation of proto-biological molecules within the mineral membranes to alter their properties for life's purposes. Here, we study a laboratory analogue of this process: chemical-garden precipitation of the amino acids arginine and tryptophan with the metal salt iron chloride and sodium silicate. We produced these chemical gardens using different methodologies in order to determine the dependence of the morphology and chemistry on the growth conditions, as well as the effect of the amino acids on the formation of the iron-silicate chemical garden. We compared the effects of having amino acids initially within the forming chemical garden, corresponding to the internal zones of hydrothermal vents, or else outside, corresponding to the surrounding ocean. The characterization of the formed chemical gardens using X-ray diffraction, Fourier transform infrared spectroscopy, elemental analysis, and scanning electron microscopy demonstrates the presence of amino acids in these structures. The growth method in which the amino acid is initially in the tablet with the iron salt is that which generated chemical gardens with more amino acids in their structures.

Microwave-Assisted Rapid Synthesis of Luminescent Tryptophan-Stabilized Silver Nanoclusters for Ultra-Sensitive Detection of Fe(III), and Their Application in a Test Strip

A new preparation method for extreme fluorescent green emission tryptophan-stabilized silver nanoclusters (Tryp-AgNCs) is presented in this scientific research. The produced silver nanoclusters are dependent on tryptophan amino acid which contributes to normal growth in infants and the sublimation and recovery of human protein, muscles, and enzymes. Herein, we have introduced a green method by using microwave-assisted rapid synthesis. The subsequent silver nanoclusters (AgNCs) have excitation/emission peaks at 408/498 nm and display a considerable selectivity to Fe(III) ions. The tryptophan amino acid molecule was used in the synthesis process as a reducing and stabilizing agent. The Tryp-AgNCs’ properties were investigated in terms of morphology, dispersity, and modification of the synthesized particles using different advanced instruments. The luminescent nanoclusters traced the Fe(III) ions by the luminescence-quenching mechanism of the Tryp-AgNCs luminescence. Therefore, the extreme selectivity of the prepared nanoclusters was exhibited to the Fe(III) ions, permitting the sensitive tracing of ferric ions in the lab and in the real environmental samples. The limit of detection for Fe(III) ions based on Tryp-AgNCs was calculated to be 16.99 nM. The Tryp-AgNCs can be efficiently applied to a paper test strip method. The synthesized nanoclusters were used efficiently to detect the Fe(III) ions in the environmental samples. Moreover, we examined the reactivity of Tryp-AgNCs on various human tumor cell lines. The results show that the Tryp-AgNCs exhibited their activity versus the cancer cells in a dose-dependent routine for the perceived performance versus the greatest-used cancer cell lines.

Amino Acids Improve Aerosolization and Chemical Stability of Potential Inhalable Amorphous Spray-dried Ceftazidime for Pseudomonas aeruginosa Lung Infection

Pseudomonas aeruginosa infection is common in cystic fibrosis as well non-cystic fibrosis bronchiectasis. The pathogen presents challenges for treatment due to its adaptive antibiotic-resistance, mainly pertaining to its biofilm-forming ability, as well as limitations associated with conventional drug delivery in achieving desired therapeutic concentration in the infection site. Hence, therapeutic approach has shifted towards the inhalation of antibiotics. Ceftazidime is a potent antibiotic against the pathogen; however, it is currently only available as a parenteral formulation. Here, spray-dryer was employed to generate inhalable high dose ceftazidime microparticles. In addition, the use of amino acids (valine, leucine, methionine, phenylalanine, and tryptophan) to improve aerosolization as well as chemical stability of amorphous ceftazidime was explored. The particles were characterized using X ray diffraction, infrared (IR) spectroscopy, calorimetry, electron microscopy, particle size analyzer, and next generation impactor. The chemical stability at 25 °C/<15% was assessed using chromatography. All co-spray dried formulations were confirmed as monophasic amorphous systems using calorimetry. In addition, principal component analysis of the IR spectra suggested potential interaction between tryptophan and ceftazidime in the co-amorphous matrix. Inclusion of amino acids improved aerosolization and chemical stability in all cases. Increase in surface asperity was clear with the use of amino acids which likely contributed to the improved aerosol performance, and potential interaction between amino acids and ceftazidime was plausibly the reason for improved chemical stability. Leucine offered the best aerosolization enhancement with a fine particle fraction of 78% and tryptophan showed stabilizing superiority by reducing chemical degradation by 51% over 10 weeks in 1:1 molar ratio. The protection against ceftazidime degradation varied with the nature of amino acids. Additionally, there was a linear relationship between degradation protection and molar mass of amino acids or percentage weight of amino acids in the formulations. None of the amino acids were successful in completely inhibiting degradation of ceftazidime in amorphous spray-dried powder to prepare a commercially viable product with desired shelf-life. All the amino acids and ceftazidime were non-toxic to A549 alveolar cell line.

Ligand-Induced Ground- and Excited-State Chirality in Silicon Nanoparticles: Surface Interactions Matter

Silicon-based light-emitting materials have emerged as a favorable substitute to various organic and inorganic systems due to silicon's high natural abundance, low toxicity, and excellent biocompatibility. However, efforts on the design of free-standing silicon nanoparticles with chiral non-racemic absorption and emission attributes are rather scare. Herein, we unravel the structural requirements for ligand-induced chirality in silicon-based nanomaterials by functionalizing with D- and L-isomers of a bifunctional ligand, namely, tryptophan. The structural aspects of these systems are established using high-resolution high-angle annular dark-field imaging in the scanning transmission electron microscopy mode, solid-state nuclear magnetic resonance, Fourier transform infrared, and X-ray photoelectron spectroscopy. Silicon nanoparticles capped with L- and D-isomers of tryptophan displayed positive and negative monosignated circular dichroic signals and circularly polarized luminescence indicating their ground- and excited-state chirality. Various studies supported by density functional theory calculations signify that the functionalization of indole ring nitrogen on the silicon surface plays a decisive role in modifying the chiroptical characteristics by generating emissive charge-transfer states. The chiroptical responses originate from the multipoint interactions of tryptophan with the nanoparticle surface through the indole nitrogen and -CO₂^- groups that can transmit an enantiomeric structural imprint on the silicon surface. However, chiroptical properties are not observed in phenylalanine- and alanine-capped silicon nanoparticles, which are devoid of Si-N bonds and chiral footprints. Thus, the ground- and excited-state chiroptics in tryptophan-capped silicon nanoparticles originates from the collective effect of ligand-bound emissive charge-transfer states and chiral footprints. Being the first report on the circularly polarized luminescence in silicon nanoparticles, this work will open newer possibilities in the field of chirality.

(Co-)amorphization of enantiomers - Investigation of the amorphization process, the physical stability and the dissolution behavior

A novel approach for improvement of the aqueous solubility of poorly water soluble compounds applying co-amorphous systems was investigated by application of the enantiomers of the chiral amino acid tryptophan (TRP) as the model system. (Co-)amorphization of various forms of crystalline TRP was achieved by ball milling. Solid state analysis demonstrated significant differences in the amorphization tendency and physical stability between the two TRP enantiomers alone, the TRP racemate and an equimolar physical mixture of D- and L-TRP (TRP conglomerate). Ball milling for 6 h was required to obtain fully amorphous plain D- and L-TRP, whereas the TRP racemate and the TRP conglomerate were transformed into their amorphous forms already within 90 and 60 min of ball milling, respectively. Physical stability of the co-amorphous TRP conglomerate was observed for up to 60 d at ambient conditions as well as 40 °C/0 % RH. In contrast, the amorphous TRP racemate showed a reduced physical stability under ambient conditions. Interestingly, the intrinsic dissolution rates of the amorphous TRP conglomerate and racemate were not higher than those of the respective crystalline forms. In conclusion, applying two enantiomers of a chiral compound may be a promising approach for fast amorphization of an API and for improving the physical stability of the resulting amorphous form.

Spectroscopic Investigations of 316L Stainless Steel under Simulated Inflammatory Conditions for Implant Applications: The Effect of Tryptophan as Corrosion Inhibitor/Hydrophobicity Marker

In this paper, the conformational changes of tryptophan (Trp) on the corroded 316 L stainless steel (SS) surface obtained under controlled simulated inflammatory conditions have been studied by Raman (RS) and Fourier-transform infrared (FT-IR) spectroscopy methods. The corrosion behavior and protective efficiency of the investigated samples were performed using the potentiodynamic polarization (PDP) technique in phosphate-buffered saline (PBS) solution acidified to pH 3.0 at 37 °C in the presence and absence of 10−2 M Trp, with different immersion times (2 h and 24 h). The amino acid is adsorbed onto the corroded SS surface mainly through the lone electron pair of the nitrogen atom of the indole ring, which adopts a more/less tilted orientation, and the protonated amine group. The visible differences in the intensity of the Fermi doublet upon adsorption of Trp onto the corroded SS surface, which is a sensitive marker of the local environment, suggested that a stronger hydrophobic environment is observed. This may result in an improvement of the corrosion resistance, after 2 h than 24 h of exposure time. The electrochemical results confirm this statement—the inhibition efficiency of Trp, acting as a mixed-type inhibitor, is made drastically higher after a short period of immersion.

Application of Alanine Scanning to Determination of Amino Acids Essential for Peptide Adsorption at the Solid/Solution Interface and Binding to the Receptor: Surface-Enhanced Raman/Infrared Spectroscopy versus Bioactivity Assays

The article describes the application of the alanine-scanning technique used in combination with Raman, surface-enhanced Raman, attenuated total reflection Fourier transform infrared, and surface-enhanced infrared absorption (SEIRA) spectroscopies, which allowed defining the role of individual amino acid residues in the C-terminal 6-14 fragment of the bombesin chain (BN6-14) on the path of its adsorption on the surface of Ag (AgNPs) and Au nanoparticles (AuNPs). A reliable analysis of the SEIRA spectra of these peptides was possible, thanks to a curve fitting of these spectra. By combining alanine-scanning with biological activity studies using cell lines overexpressing bombesin receptors and the intracellular inositol monophosphate assay, it was possible to determine which peptide side chains play a significant role in binding a peptide to membrane-bound G protein-coupled receptors (GPCRs). Based on the analysis of spectral profiles and bioactivity results, conclusions for the specific peptide-metal and peptide-GPCR interactions were drawn and compared.

Is the Use of Surface-Enhanced Infrared Spectroscopy Justified in the Selection of Peptide Fragments That Play a Role in Substrate-Receptor Interactions? Adsorption of Amino Acids and Neurotransmitters on Colloidal Ag and Au Nanoparticles

This paper describes an application of attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and surface-enhanced infrared spectroscopy (SEIRA) to characterize the selective adsorption of four peptides present in body fluids such as neuromedin B (NMB), bombesin (BN), neurotensin (NT), and bradykinin (BK), which are known as markers for various human carcinomas. To perform a reliable analysis of the SERIA spectra of these peptides, curve fitting of these spectra in the spectral region above 1500 cm^–1 and SEIRA measurements of sulfur-containing and aromatic amino acids were performed. On the basis of the analyses of the spectral profiles, specific conclusions were drawn regarding specific molecule–metal interactions and changes in the interaction during the substrate change from the surface of silver nanoparticles (AgNPs) to gold nanoparticles (AuNPs).

Physico-chemical interactions of a new rod-coil-rod polymer with liposomal system: Approaches to applications in tryptophan-related therapies

This work describes the synthesis of the new supramolecular rod-coil-rod polymer, designated as cholesterol-PEO₁₀₀₀-tryptophan (Chl-PEO-Trp), as well as its effects on the physico-chemical properties of phosphatidylcholine (PC)-based liposomes. The molecular interactions between the Chl-PEO-Trp and PC were characterized by HATR-FTIR, DSC, NMR, DLS and zeta (ζ) potential techniques. The Chl-PEO-Trp polymer yield was 75 %. FTIR and DSC data showed that the motion of almost all PC groups was restricted by the polymer, and it promoted a decrease of the trans-gauche isomerization of the PC methylene, restricting the mobility of the hydrophobic region of the liposomes. NMR analyses indicated a Chl-PEO-Trp-induced restriction in the rotation of the PC phosphorus and a discreet increase of the hydrogen mobility of the choline. Despite this increase in the rotation of the choline, DLS and ζ-potential analyses suggested a reorientation of the choline group toward the system surface, which contributed, along with the other physico-chemical effects, to a globally packed membrane arrangement and reduced liposome size. Data described in this work were correlated to possible applications of the Chl-PEO-Trp in its free or PC liposome-loaded forms in the diagnosis and therapy of cancer, SARS caused by coronaviruses, and central nervous system-related diseases.

Co-Amorphization of Kanamycin with Amino Acids Improves Aerosolization

Different formulation techniques have been investigated to prepare highly aerosolizable dry powders to deliver a high dose of antibiotics to the lung for treating local infections. In this study, we investigated the influence of the co-amorphization of a model drug, kanamycin, with selected amino acids (valine, methionine, phenylalanine, and tryptophan) by co-spray drying on its aerosolization. The co-amorphicity was confirmed by thermal technique. The physical stability was monitored using low-frequency Raman spectroscopy coupled with principal component analysis. Except for the kanamycin-valine formulation, all the formulations offered improved fine particle fraction (FPF) with the highest FPF of 84% achieved for the kanamycin-methionine formulation. All the co-amorphous formulations were physically stable for 28 days at low relative humidity (25 °C/<15% RH) and exhibited stable aerosolization. At higher RH (53%), even though methionine transformed into its crystalline counterpart, the kanamycin-methionine formulation offered the best aerosolization stability without any decrease in FPF. While further studies are warranted to reveal the underlying mechanism, this study reports that the co-amorphization of kanamycin with amino acids, especially with methionine, has the potential to be developed as a high dose kanamycin dry powder formulation.

Planarity and out-of-plane vibrational modes of tryptophan and tyrosine in biomolecular modeling

Tryptophan and tyrosine are amino acids that play significant roles in the folding processes of proteins at water-membrane interfaces because of their amphipathic heteroaromatic rings. Employing appropriate heteroaromatic molecular structures is essential for obtaining accurate dynamics and predictive capabilities in molecular simulations of these amino acids. In this study, molecular dynamics simulations that applied the most recent version of the CHARMM36 force field were conducted on aqueous solutions of tryptophan and of tyrosine. Geometric analysis and dynamics quantified how aromatic rings deviated from planar structures and exhibited out-of-plane fluctuations. Radial distribution functions showed possible biological significance because the extent of ring planarity slightly affected local water concentrations near aromatic rings. Instantaneous all-atom normal mode analysis (NMA) and Fourier transformation of time autocorrelation functions of out-of-plane displacements were applied to study out-of-plane vibrations of atoms in these rings. The NMA started with minimum energy configurations and then averaged over fluctuations in aqueous solution. The frequencies and frequency patterns that were obtained for tryptophan and tyrosine with CHARMM36 differed from literature reports of Raman spectra, infrared spectra, and frequencies calculated using quantum mechanics, with some out-of-plane modes found at higher frequencies. Effects of imposing improper torsion potentials and changing torsion angle force constants were investigated for all atoms in the rings of tryptophan and tyrosine. Results show that these coarse force field variations only affect planarity and out-of-plane vibrations of atoms within the rings, and not other vibrations. Although increasing improper torsion force constants reduced deviations from aromatic ring planarity significantly, it increased out-of-plane mode frequencies. Reducing torsion angle force constants (with and without improper torsions) shifted modes to lower frequencies. A combination of decreasing most torsion angle force constants for ring atoms in both amino acids and including improper torsion forces attained frequencies and frequency patterns for out-of-plane normal modes that were more similar to the literature spectra. These force field variations decreased the extents of out-of-plane vibrations within the heteroaromatic rings of tryptophan, especially around the nitrogen atom in the ring, but not within the heteroaromatic ring of tyrosine. Conclusions were unaffected by the peptide endgroup, water, or simulation ensemble.

Conformational Changes and Charge Transfer in Biomolecules Resolved Using Dynamic Enhanced Raman Correlation Spectroscopy

In this contribution, we report that conformational changes of molecules that are often buried in a wide-distributed Gaussian distribution can be discerned by analyzing the dynamics of specific Raman lines. We investigate the pertinence of the auto- and cross-correlation functions applied to the dynamics of three Raman lines of an amino acid, the tryptophan. The cross-correlation between intensity and the Raman band is an indicator of the charge transfer during the diffusion limited reaction of tryptophan and the gold surface. The Péclet number Pe can provide a valuable indicator of the convective and/or diffusive features of each Raman band. Adsorption induced conformation changes can be identified using the autocorrelation of the multiples states within the Raman band centered at 1550 cm^-1.

Synthesis, characterization, theoretical studies and biological (antioxidant, anticancer, toxicity and neuroprotective) determinations of a copper(II) complex with 5-hydroxytryptophan

5-Hydroxy-L-tryptophan (5-HTP) is a serotonin pathway metabolite of L-tryptophan in the brain. In the knowledge that the biological properties of some compounds can be modified upon metal complexation, a new solid metal complex, [Cu(5-hydroxytryptophan)₂].H₂O (Cu5HTP), has been synthesized and characterized to analyze the modification of some biological properties. The conformational investigations (optimized in gas phase at B3LYP/6-311G** theory level) suggest the coexistence of two conformers of Cu5HTP with cis- and trans- arrangements of the amino acids in the equatorial plane. The trans- Cu5HTP1 complex is the most stable conformer. The complexation led to an enhancement of the antioxidant properties of the ligand. The metal complex also improved the anticancer behavior of the ligand (tested in cancer cell lines derived from human lung (A549), cervix (HeLa) and colon (HCT-116)). It did not show toxicity against either the non-malignant human lung fibroblast (MRC-5) cell line or Artemia salina and did not behave as mutagenic agent (Ames test). Cellular reactive oxygen species production may be one of the possible mechanisms of action. Besides, the metal complex exerted neuroprotective action on cortical neurons from embryonic 18 days rats exposed to glutamate.

Tracking hidden organic carbon in rocks using chemometrics and hyperspectral imaging

Finding traces of life or organic components of prebiotic interest in the rock record is an appealing goal for numerous fields in Earth and space sciences. However, this is often hampered by the scarceness and highly heterogeneous distribution of organic compounds within rocks. We assess here an innovative analytical strategy combining Synchrotron radiation-based Fourier-Transform Infrared microspectroscopy (S-FTIR) and multivariate analysis techniques to track and characterize organic compounds at the pore level in complex oceanic rocks. S-FTIR hyperspectral images are analysed individually or as multiple image combinations (multiset analysis) using Principal Component Analyses (PCA) and Multivariate Curve Resolution – Alternating Least Squares (MCR-ALS). This approach allows extracting simultaneously pure organic and mineral spectral signatures and determining their spatial distributions and relationships. MCR-ALS analysis provides resolved S-FTIR signatures of 8 pure mineral and organic components showing the close association at a micrometric scale of organic compounds and secondary clays formed during rock alteration and known to catalyse organic synthesis. These results highlights the potential of the serpentinizing oceanic lithosphere to generate and preserve organic compounds of abiotic origin, in favour of the hydrothermal theory for the origin of life.

L-tryptophan L-tryptophanium chloride

L-tryptophan L-tryptophanium chloride is a new salt with (A⋯A(+)) type dimeric cation. It crystallizes in the monoclinic system (space group P2(1), Z=2). The asymmetric unit contains one zwitterionic L-tryptophan molecule, one L-tryptophanium cation and one chloride anion. The dimeric cation is formed by a O-H⋯O hydrogen bond with the O⋯O distance equal to 2.5556(18) Å. The infrared and Raman spectra of the crystal are studied and compared with the spectra of L-tryptophanium chloride.

Improving co-amorphous drug formulations by the addition of the highly water soluble amino Acid, proline

Co-amorphous drug amino acid mixtures were previously shown to be a promising approach to create physically stable amorphous systems with the improved dissolution properties of poorly water-soluble drugs. The aim of this work was to expand the co-amorphous drug amino acid mixture approach by combining the model drug, naproxen (NAP), with an amino acid to physically stabilize the co-amorphous system (tryptophan, TRP, or arginine, ARG) and a second highly soluble amino acid (proline, PRO) for an additional improvement of the dissolution rate. Co-amorphous drug-amino acid blends were prepared by ball milling and investigated for solid state characteristics, stability and the dissolution rate enhancement of NAP. All co-amorphous mixtures were stable at room temperature and 40 °C for a minimum of 84 days. PRO acted as a stabilizer for the co-amorphous system, including NAP–TRP, through enhancing the molecular interactions in the form of hydrogen bonds between all three components in the mixture. A salt formation between the acidic drug, NAP, and the basic amino acid, ARG, was found in co-amorphous NAP–ARG. In comparison to crystalline NAP, binary NAP–TRP and NAP–ARG, it could be shown that the highly soluble amino acid, PRO, improved the dissolution rate of NAP from the ternary co-amorphous systems in combination with either TRP or ARG. In conclusion, both the solubility of the amino acid and potential interactions between the molecules are critical parameters to consider in the development of co-amorphous formulations.

Amino acids as co-amorphous stabilizers for poorly water-soluble drugs--Part 2: molecular interactions

The formation of co-amorphous drug-drug mixtures has proved to be a powerful approach to stabilize the amorphous form and at the same time increase the dissolution of poorly water-soluble drugs. Molecular interactions in these co-amorphous formulations can play a crucial role in stabilization and dissolution enhancement. In this regard, Fourier-transform infrared spectroscopy (FTIR) is a valuable tool to analyze the molecular near range order of the compounds in the co-amorphous mixtures. In this study, several co-amorphous drugs--low molecular weight excipient blends--have been analyzed with FTIR spectroscopy. Molecular interactions of the drugs carbamazepine and indomethacin with the amino acids arginine, phenylalanine, and tryptophan were investigated. The amino acids were chosen from the biological target site of both drugs and prepared as co-amorphous formulations together with the drugs by vibrational ball milling. A detailed analysis of the FTIR spectra of these formulations revealed specific peak shifts in the vibrational modes of functional groups of drug and amino acid, as long as one amino acid from the biological target site was present in the blends. These peak shifts indicate that the drugs formed specific molecular interactions (hydrogen bonding and π-π interactions) with the amino acids. In the drug-amino acid mixtures that contained amino acids which were not present at the biological target site, no such interactions were identified. This study shows the potential of amino acids as small molecular weight excipients in co-amorphous formulations to stabilize the amorphous form of a poorly water-soluble drug through strong and specific molecular interactions with the drug.

Combined FTIR Matrix Isolation and Density Functional Studies of Indole-3-Pyruvic Acid Molecule. Spectroscopic Evidence of Gas-Phase Tautomerism

The vibrational spectrum of matrix-isolated indole-3-pyruvic acid has been studied aiming to obtain information about the structures of the stable vapour-phase forms of the molecule. Together with results from theoretical density functional calculations, the spectroscopic data enable to undertake an attribution for most of the observed bands. The FTIR spectrum of crystalline indole-3-pyruvic acid has been compared with that of matrix isolation study.

Study on monomer suitability toward the template in molecularly imprinted polymer: an ab initio approach

Study of monomer-template interactions in molecularly imprinted polymer (MIP) is inevitable to comprehend best selectivity at the molecular level in pre-polymer solution. In the present work, binding energies of tryptophan, an amino acid template, complexed with different monomers were computed using second order Moller Plesset theory (MP2) at 6-311++g** level in gas phase. This helped in recommending a generic MIP, suitable for the selective and sensitive diagnosis of tryptophan, in clinical setting as disease biomarker, at primitive level. The tryptophan is an important biomarker owing to its highly regulated physiological process in the treatment of premenstrual dysphoric disorder and pellagra like diseases. Frequency calculations were performed using Density Functional Theory (DFT) at B3LYP employing 6-31+g (2d, 2p) level including thermal and entropy corrections. The monomer, p-nitrophenyl acrylate (2 mol), was adjudged having giving best binding score for the complexation at ground state with tryptophan (1 mol) for MIP development.

An experimental and theoretical study of L-Tryptophan in an aqueous solution, combining two-layered ONIOM and SCRF calculations

ONIOM and SCRF calculations were performed to study the most stable theoretical structure of L-tryptophan in an aqueous solution phase and to observe the changes occurring in the structural and vibrational properties of L-tryptophan in the aqueous media. L-Tryptophan was characterized by infrared and Raman spectroscopies in the solid state and as an aqueous solution. Optimized geometries and relative stabilities for the L-tryptophan zwitterion were calculated while taking into account solvent effects using the self-consistent reaction field (SCRF) theory. The obtained results in the aqueous solution were compared with those calculated for the zwitterion in the gas phase by means of two-layered ONIOM calculations. For the complete assignments of the IR and Raman spectra of L-tryptophan in the aqueous solution phase, density functional theory (DFT) calculations were combined with Pulay's scaled quantum mechanical force field (SQMFF) methodology in order to fit the theoretical wavenumber values to the experimental values. Additionally, the roles of specific and bulk contributions from solvent effects on the properties of l-tryptophan were analyzed. Furthermore, bands corresponding to the normal modes of vibration were localized and assigned, and they served as the bases for the calculations of the corresponding force constants. Significant effects on the geometrical and vibrational frequencies were found for the studied zwitterion.

Structure of monolayers formed from neurotensin and its single-site mutants: vibrational spectroscopic studies

The human, pig, and frog neurotensins and four single-site mutants of human neurotensin (NT), having the following modifications, [Gln(4)]NT, [Trp(11)]NT, [D-Trp(11)]NT, and [D-Tyr(11)]NT, were immobilized onto an electrochemically roughened silver electrode surface in an aqueous solution. The orientation of adsorbed molecules was determined from surface-enhanced Raman scattering (SERS) measurements. A comparison was made between these structures to determine how the change upon the mutation of the neurotensin structure influences its adsorption properties. The SERS patterns were correlated with the contribution of the structural components of the aforementioned peptides to the ability to interact with the NTR1 G-protein receptor. Briefly, the SERS spectra revealed that the substitution of native amino acids in investigated peptides influenced slightly their adsorption state on an electrochemically roughened silver surface. Thus, human, pig, and frog neurotensins and [Gln(4)]NT and [D-Tyr(11)]NT tended to adsorb to the surface via the tyrosine ring, the oxygen atom of the deprotonated phenol group of Tyr(11), and the -CH(2)- unit(s), most probably of Tyr(11), Arg(9), and/or Leu(13). The observed changes in the enhancement of the deprotonated Tyr residue SERS signals indicated a further parallel orientation of a phenol-O bond with regard to the silver surface normal for pig NT, [Gln(4)]NT, and [D-Tyr(11)]NT, whereas the orientation was slightly tilted for human and frog NT. In the case of [Trp(11)]NT and [D-Trp(11)]NT, the formation of a peptide/Ag complex was confirmed by strong SERS bands involving the phenyl co-ring of Trp(11)/d-Trp(11) and -CH(2)- vibrations and the tilted and flat orientations of the two compounds with respect to the surface substrate. The spectral features were accompanied by a SERS signal caused by vibrations of the carboxyl group of C-terminal Leu(13) and the guanidine group of Arg(9). Reported changes in SERS spectra of L and D isomers were fully supported by generalized two-dimensional correlation analysis. Additionally, a combination of mutation-labeling and vibrational spectroscopy (Fourier-transform Raman and absorption infrared) was used to investigate the possible peptide conformations and environments of the tyrosine residues.

Analysis of measured and calculated Raman spectra of indole, 3-methylindole, and tryptophan on the basis of observed and predicted isotope shifts

The aromatic amino acid tryptophan plays an important role in protein electron-transfer and in enzyme catalysis. Tryptophan is also used as a probe of its local protein environment and of dynamic changes in this environment. Raman spectroscopy of tryptophan has been an important tool to monitor tryptophan, its radicals, and its protein environment. The proper interpretation of the Raman spectra requires not only the correct assignment of Raman bands to vibrational normal modes but also the correct identification of the Raman bands in the spectrum. A significant amount of experimental and computational work has been devoted to this problem, but inconsistencies still persist. In this work, the Raman spectra of indole, 3-methylindole (3MI), tryptophan, and several of their isotopomers have been measured to determine the isotope shifts of the Raman bands. Density functional theory calculations with the B3LYP functional and the 6-311+G(d,p) basis set have been performed on indole, 3MI, 3-ethylindole (3EI), and several of their isotopomers to predict isotope shifts of the vibrational normal modes. Comparison of the observed and predicted isotope shifts results in a consistent assignment of Raman bands to vibrational normal modes that can be used for both assignment and identification of the Raman bands. For correct assignments, it is important to determine force field scaling factors for each molecule separately, and scaling factors of 0.9824, 0.9843, and 0.9857 are determined for indole, 3MI, and 3EI, respectively. It is also important to use more than one parameter to assign vibrational normal modes to Raman bands, for example, the inclusion of isotope shifts other than those obtained from H/D-exchange. Finally, the results indicate that the Fermi doublet of indole may consist of just two fundamentals, whereas one fundamental and one combination band are identified for the Fermi resonance that gives rise to the doublet in 3MI and tryptophan.

Clarification of the binding model of lead(II) with a highly sensitive and selective fluoroionophore sensor by spectroscopic and structural study

The detection of lead ion is very important both in environment and in biological systems because of its toxicity. A fluoroionophore sensor, N-[4(1-pyrene)-butyroyl]-l-tryptophan (PLT), distinguishing Pb(2+) from other 12 metal ions and exhibiting a very high sensitivity (0.15microM) in aqueous solution, has been reported. The present study describes the spectroscopic clarification of the intrinsic differences of the binding model between PLT with Pb(2+) and with other ions. The fluorescent property of solid metal carboxylates reflects a character of the metal complex in solution, which results in a facility to solve problems by using solid sample of complex and vibrational spectroscopy. Both FT-infrared and Raman spectroscopy are employed to clarify the binding model between lead ion and its high sensitive and selective fluoroionophore sensor PLT, and essentially to explain why the metal ions other than Pb(2+) cannot response to PLT. The IR spectral data clearly show that a bridging bidentate coordination occurs when PLT is coordinated with Cu(2+) and Zn(2+); while a chelating bidentate coordination between the carboxyl anion and Pb(2+) exists in PLT-Pb, which is a new information beyond the NMR results in previous report. Meanwhile, the present study also indicates a characteristic interaction of lead ion and indole ring as well as the hydrogen bonding between amide groups. Furthermore, the quantum chemical calculations at the DFT level confirm the spectral and structural information of PLT-Pb(2+) proposed by experiments. Thus, the type of coordination, the interaction of the indole ring with the metal ion, and the hydrogen bonding between amide groups in PLT-Pb are likely responsible for the high selectivity of PLT to the lead(II) ion.

Surface-enhanced Raman difference between bombesin and its modified analogues on the colloidal and electrochemically roughen silver surfaces

In this article, surface-enhanced Raman scattering (SERS) spectra of bombesin (BN) and its six modified analogues ([D-Phe(12)]BN, [Tyr(4)]BN, [Tyr(4),D-Phe(12)]BN, [D-Phe(12),Leu(14)]BN, [Leu(13)-(R)-Leu(14)]BN, and [Lys(3)]BN) on a colloidal silver surface are reported and compared with SERS spectra of these species immobilized onto an ellectrochemically roughen silver electrode. Changes in enhancement and wavenumber of proper bands upon adsorption on different silver surfaces are consistent with BN and its analogues adsorption primarily through Trp(8). Slightly different adsorption states of these molecules are observed depending upon natural amino acids substitution. For example, the indole ring in all the peptides interacts with silver nanoparticles in a edge-on orientation. It is additionally coordinated to the silver through the N(1)--H bond for all the peptides, except [Phe(12)]BN. This is in contrary to the results obtained for the silver roughen electrode that show direct but not strong N(1)--H/Ag interaction for all peptides except [D-Phe(12),Leu(14)]BN and [Leu(13)-(R)-Leu(14)]BN. For BN only C==O is not involved in the chemical coordination with the colloidal surface. [Lys(3)]BN and BN also adsorb with the C--N bond of NH(2) group normal and horizontal, respectively, to the colloidal surface, whereas C--NH(2) in other peptides is tilted to this surface. Also, the Trp(8) --CH(2)-- moiety of only [Tyr(4)]BN, [Lys(3)]BN, and [Tyr(4),D-Phe(12)]BN coordinates to Ag, whereas the Phe(12) ring of [Phe(12)]BN, [Tyr(4),D-Phe(12)]BN, and [D-Phe(12),Leu(14)]BN assists in the peptides binding only on the colloidal silver.