Seven Conformers of Neutral Dopamine Revealed in the Gas Phase

Micro Solvation Effect of Methanol on Excited-State Dynamics of Protonated Tryptophan and Dopamine

The electronic and vibrational cryogenic ion spectroscopy of protonated tryptophan (TrpH+) and dopamine (DAH+) complexed with methanol has been recorded. These two biological chromophores exhibit ultrafast photochemistry due to excited-state proton transfer (ESPT). We have established the relationship between the structure of the complexes and their photodynamics and compared them with recent results obtained in hydrated complexes. For TrpH+, there is no substantial change between methanol and water complexes; ESPT is hindered by a single solvent molecule. In the DAH+(MeOH)1 complex, the most stable conformer adopts a structure that prevents the direct interaction of the ammonium group of the side chain with the catechol ring, thus blocking the ESPT reaction. Such a ring structure is indeed a very minor populated conformer in the single-hydrated complex. The change in conformal stability between water and methanol clusters is due to a weak CH-π attractive interaction of the methyl group of methanol with the catechol.

A journey across dopamine Metabolism: A rotational study of DOPAC

DOPAC, a relevant scaffold in dopamine metabolism, was probed in the gas phase and interrogated by high-resolution rotational spectroscopy. Herein, three distinct conformers were isolated in a supersonic jet and identified for the first time through an examination of the trend of the rotational constants and the dipole moment selection rules. Additionally, we examined the plausible relaxation pathways of the low-energy conformers of DOPAC, which helped us to claim the indirect detection of two additional conformers, providing conclusive experimental evidence of the flexible nature of this biomolecule. The current investigation sheds some light on the differences between jet-cooled rotational experiments and matrix-isolation infrared spectroscopy.

Intramolecular interactions (O-H∙∙∙O, C-H∙∙∙N, N-H∙∙∙π) in isomers of neutral, cation, and anion dopamine molecules: A DFT study on the influence of solvents (water and ethanol)

CONTEXT

Dopamine (DA) is one of the most important neurotransmitters associated with numerous neural disorders. This investigation reports the intramolecular interactions present in the isomers of neutral (DA⁰), anionic (DA^-), and cationic (DA⁺) dopamine isomers in gas, water, and ethanol mediums. Neutral and anion isomers have O-H∙∙∙O, C-H∙∙∙N intramolecular hydrogen bonds and N-H∙∙∙π interactions. All the interactions are electrostatic in nature. Isomers of cation dopamine show no intramolecular interactions in the solvent. Natural charges from natural bond orbital (NBO) analysis show that O-H∙∙∙O bonds and the N-H∙∙∙π interactions are the most and least polar, respectively. ¹H NMR study reveals the inverse linear correlation between shielding constant and electron density in a solvent medium. HOMO-LUMO energy gap indicates higher stability for neutral and cationic forms of dopamine isomers in water and ethanol medium.

METHODS

We have optimized all the structural forms of dopamine molecule using the Becke three hybrid exchange and Lee-Yang-Parr correlation functional with Grimme's dispersion correction, B3LYP-D3(BJ), and aug-cc-pVTZ basis set using the Gaussian16 software. Vibrational frequency analysis with no imaginary frequencies confirms the nature of global minima. The solvent studies (water and ethanol) were carried out using the SCRF keyword and the polarisable continuum model (PCM) of Miertus and Tomasi. NBO analysis and NMR studies were also performed for all conformers. Topology analysis was explored using the software Multiwfn.

Excited state dynamics of protonated dopamine: hydration and conformation effects

Electronic and vibrational spectroscopy in a cryogenic ion trap has been applied to protonated dopamine water clusters and assigned with the help of quantum chemistry calculations performed in the ground and electronic excited states. A dramatic hydration effect is observed when dopamine is solvated by three water molecules. The broad electronic spectra recorded for the bare and small water clusters containing protonated dopamine turn to sharp, well-resolved vibronic transitions in the 1-3 complex. This reflects the change induced by hydration in the photodynamics of protonated dopamine which is initially controlled by an excited state proton transfer (ESPT) reaction from the ammonium group toward the catechol ring. Interestingly, conformer selectivity is revealed in the 1-3 complex which shows two low lying energy conformers for which the ESPT reaction is prevented or not depending on the H-bond network formed between the dopamine and water molecules.

Shape‐Shifting Molecules: Unveiling the Valence Tautomerism Phenomena in Bare Barbaralones

We report a state‐of‐the‐art spectroscopic study of an archetypical barbaralone, conclusively revealing the valence tautomerism phenomena for this bistable molecular system. The two distinct 1‐ and 5‐substituted valence tautomers have been isolated in a supersonic expansion for the first time and successfully characterized by high‐resolution rotational spectroscopy. This work provides irrefutable experimental evidence of the [3,3]‐rearrangement in barbaralones and highlights the use of rotational spectroscopy to analyze shape‐shifting mixtures. Moreover, this observation opens the window toward the characterization of new fluxional systems in the isolation conditions of the gas phase and should serve as a reference point in the general understanding of valence tautomerism.

Dopamine Adsorption on Rutile TiO2(110): Geometry, Thermodynamics, and Core-Level Shifts from First Principles

The modification of the rutile TiO₂(110) surface with dopamine represents the best example of the functionalization of TiO₂-based nanoparticles with catecholamines, which is of great interest for sunlight harvesting and drug delivery. However, there is little information on the dopamine-TiO₂(110) adsorption complex in terms of thermodynamic properties and structural parameters such as bond coordination and orientation of the terminal ethyl-amino group. Here, we report a density functional theory (DFT) investigation of dopamine adsorption on the TiO₂(110) surface using the optB86b-vdW functional with a Hubbard-type correction to the Ti 3d orbitals, where U _eff = 3 eV. Guided by available X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) data, our simulations identify enolate species with bidentate coordination at a submonolayer coverage, which are bonded to two neighboring 5-fold-coordinated Ti atoms at the TiO₂(110) surface through both deprotonated oxygen atoms of the dopamine, i.e., in a bridging fashion. The process is highly exothermic, involving an adsorption energy of -2.90 eV. Calculated structural parameters suggest that the molecule sits approximately upright on the surface with the amino group interacting with the π-like orbitals of the aromatic ring, leading to a gauche-like configuration. The resulting NH···π hydrogen bond in this configuration can be broken by overcoming an energy barrier of 0.22 eV; in this way, the amino group rotation leads to an anti-like conformation, making this terminal group able to bind to other biomolecules. This mechanism is endothermic by 0.07 eV. Comparison of existing spectroscopic data with DFT modeling shows that our computational setup can reproduce most experimentally determined parameters such as tilt angles from NEXAFS and chemical shifts in XPS, which allows us to identify the preferred mode of adsorption of dopamine on the TiO₂(110) surface.

Unleashing the shape of L-DOPA at last

Herein, we report the first rotational study of neutral L-DOPA, an extensively used supramolecular synthon and an amino acid precursor of the neurotransmitters dopamine, norepinephrine (noradrenaline), and epinephrine (adrenaline) using broadband and narrowband Fourier transform microwave spectroscopies coupled with a laser ablation vaporization system. The spectroscopic parameters derived from the analysis of the rotational spectrum conclusively identify the existence of four distinct conformers of L-DOPA in the supersonic jet, further rejecting the previously reported catechol ring-induced conformational restriction. The analysis of the ¹⁴N nuclear quadrupole coupling hyperfine structure further revealed the orientation of the N-bearing functional group, proving the existence of stabilizing N-H⋯π interactions for the observed structures.

Structural and Energetic Properties of Amino Acids and Peptides Benchmarked by Accurate Theoretical and Experimental Data

Structural, energetic, and spectroscopic data derived in this work aim at the setup of an "experimentally validated" database for amino acids and polypeptides conformers. First, the "cheap" composite scheme (ChS, CCSD(T)/(CBS+CV)^MP2) is tested for evaluation of conformational energies of all eight stable conformers of glycine, by comparing to the more accurate CCSD(T)/CBS+CV computations (Phys. Chem. Chem. Phys. 2013, 15, 10094-10111 and J Mol. Model. 2020, 26, 129). The recently proposed jun-ChS (J. Chem. Theory and Comput. 2020, 16, 988-1006), employing the jun-cc-pVnZ basis set family for CCSD(T) computations and CBS extrapolation, yields conformational energies accurate to 0.2 kJ·mol^-1, at reduced computational cost with respect to aug-ChS employing aug-cc-pVnZ basis sets. The jun-ChS composite scheme is further applied to derive conformational energies for three dipeptide analogues Ac-Gly-NH₂, Ac-Ala-NH₂, and Gly-Gly. Finally, dipeptide conformational energies and semiexperimental equilibrium rotational constants along with the CCSD(T)/(CBS+CV)^MP2 structural parameters (J. Phys. Chem. Lett. 2014, 5, 534-540) stand as the reference for benchmarking of selected density functional methodologies. The double-hybrid functionals B2-PLYP-D3(BJ) and DSD-PBEP86, perform best for structural and energetic characterization of all dipeptide analogues. From hybrid functionals CAM-B3LYP-D3(BJ) and ωB97X-D3(BJ) represent promising methods applicable for larger peptide-based systems for which computations with double-hybrid functionals are not feasible.

Hydration-controlled excited-state relaxation in protonated dopamine studied by cryogenic ion spectroscopy

Ultraviolet (UV) and infrared (IR) spectra of protonated dopamine (DAH⁺) and its hydrated clusters DAH⁺(H₂O)_1-3 are measured by cryogenic ion spectroscopy. DAH⁺ monomer and hydrated clusters with up to two water molecules show a broad UV spectrum, while it turns to a sharp, well-resolved one for DAH⁺-(H₂O)₃. Excited state calculations of DAH⁺(H₂O)₃ reproduce these spectral features. The conformer-selected IR spectrum of DAH⁺(H₂O)₃ is measured by IR dip spectroscopy, and its structure is assigned with the help of quantum chemical calculations. The excited state lifetime of DAH⁺ is much shorter than 20 ps, the cross correlation of the ps lasers, revealing a fast relaxation dynamics. The minimal energy path along the NH → π proton transfer coordinate exhibits a low energy barrier in the monomer, while this path is blocked by the high energy barrier in DAH⁺(H₂O)₃. It is concluded that the excited state proton transfer in DAH⁺ is inhibited by water-insertion.

Broadband terahertz signatures and vibrations of dopamine

Dopamine (DA) is an essential neurotransmitter and hormone of the nervous system, its structural and conformational properties play critical roles in biological functions and signal transmission processes. Although this neuroactive molecule has been studied extensively, the low-frequency vibration features that are closely related to the conformation and molecular interactions in the terahertz (THz) band still remain unclear. In this study, a broadband THz time-domain spectroscopy (THz-TDS) system in the frequency band of 0.5-18 THz was used to characterize the unique THz fingerprint of DA. In addition, density functional theory (DFT) calculations were performed to analyze the vibrational properties of DA. The results suggest that each THz resonant absorption peak of DA corresponds to specific vibrational modes, and the collective vibration also exists in the broadband THz range. Moreover, the interactions between the DA ligand and the D2 and D3 receptors were investigated by docking, and the simulated THz spectra were obtained. The results indicate the dominant role of hydrogen bonding interactions and the specificity of molecular conformation. This work may help to understand the resonance coupling between THz electromagnetic waves and neurotransmitters.

Time-resolved neurotransmitter detection in mouse brain tissue using an artificial intelligence-nanogap

The analysis of neurotransmitters in the brain helps to understand brain functions and diagnose Parkinson’s disease. Pharmacological inhibition experiments, electrophysiological measurement of action potentials, and mass analysers have been applied for this purpose; however, these techniques do not allow direct neurotransmitter detection with good temporal resolution by using nanometre-sized electrodes. Hence, we developed a method for direct observation of a single neurotransmitter molecule with a gap width of ≤ 1 nm and on the millisecond time scale. It consists of measuring the tunnelling current that flows through a single-molecule by using nanogap electrodes and machine learning analysis. Using this method, we identified dopamine, serotonin, and norepinephrine neurotransmitters with high accuracy at the single-molecule level. The analysis of the mouse striatum and cerebral cortex revealed the order of concentration of the three neurotransmitters. Our method will be developed to investigate the neurotransmitter distribution in the brain with good temporal resolution.

Elucidating the multiple structures of pipecolic acid by rotational spectroscopy

The complex conformational space of the non-proteinogenic cyclic amino acid pipecolic acid has been explored in the gas phase for the first time. Solid pipecolic acid samples were vaporized by laser ablation and expanded in a supersonic jet where the rotational spectral signatures owing to nine different conformers were observed by Fourier transform microwave spectroscopy. All species were identified by comparison of the experimental rotational and nuclear quadrupole coupling constants with those predicted theoretically. Observation of type-III conformers, leading to a difference when compared against the conformational behavior of the analog amino acid proline, has been interpreted by an increment in steric hindrance when increasing the number of carbons present in the ring.

Structural and vibrational study of a neurotransmitter molecule: Dopamine [4-(2-aminoethyl) benzene-1,2-diol]

Structural and vibrational studies for the most stable conformer of dopamine {4-(2-Aminoethyl) benzene-1, 2-diol} have been carried out at the DFT/B3LYP/6-311++G** level using the Gaussian 09 software. The IR and Raman spectra have been recorded and analyzed in light of the computed vibrational parameters using the DFT and the PEDs computed with the help of the GAR2PED software. Some of the fundamentals have considerably changed frequencies in going from benzene to dopamine. Except the rocking and wagging modes of the NH₂ group the other four modes are pure group modes. The rocking and wagging modes of the NH₂ group show mixing with the other modes. The two OH stretching vibrations are highly localized modes. The Kekule phenyl ring stretching mode is found to remain almost unchanged. The HOMO-LUMO study suggests the existence of charge transfer within the molecule and the energy gap supports the pharmacological active property of the dopamine molecule. The NBO analysis has been carried out to understand the proper and improper hydrogen bonding.

A conformational study of protonated noradrenaline by UV–UV and IR dip double resonance laser spectroscopy combined with an electrospray and a cold ion trap method

In protonated noradrenaline, 3 folded and 2 extended conformers were identified under the ultra-cold condition.

Gas phase ultraviolet and infrared spectroscopy on a partial peptide of β2-adrenoceptor SIVSF-NH2 by a laser desorption supersonic jet technique

Laser desorption supersonic jet laser spectroscopy has been applied to a penta-peptide, Ser-Ile-Val-Ser-Phe-NH₂ (SIVSF-NH₂), which is a partial sequence of a binding site in a β₂-adrenaline receptor protein.

Structural motifs of 2-(2-fluoro-phenyl)-ethylamine conformers

Vibronic and vibrational spectra of 2-(2-fluoro-phenyl)-ethylamine (2-FPEA) conformers were measured in a molecular beam by resonant two-photon ionization (R2PI), ultraviolet–ultraviolet hole burning (UV–UV HB) spectroscopy, and ionization-loss stimulated Raman spectroscopy (ILSRS).

CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study

The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC calculations.

Conformational preferences of 3,4-dihydroxyphenylacetic acid (DOPAC)

The conformational space of 3,4-dihydroxyphenylacetic acid (DOPAC), an important dopamine metabolite, has been investigated by quantum chemical methods (B3LYP and MP2, with the 6-311++G(d,p) basis set) and matrix-isolation infrared spectroscopy. Detailed analysis of the calculated potential energy surfaces of the molecule led to identification of thirteen unique conformers, all of them showing the acetic acid side chain out of the aromatic ring plane by 60-95°. According to the calculated Gibbs energies, the five lowest energy conformers make up 99.7% of the conformational mixture at 298.15K, exhibiting individual populations falling between 16% and 24%. The main conformational trends of this molecule were interpreted on the grounds of a thorough analysis of the structural parameters and by the application of the Natural Bond Orbital theory. The role of the intramolecular interactions on the relative stability and structure of the conformers was also investigated. The infrared spectrum of DOPAC was registered after isolation of its monomers in argon and xenon matrices. Only one of DOPAC forms populated in the gas phase could be trapped in both matrix gases. This result is in agreement with the predicted low energy barriers for conformational isomerization and is also supported by annealing experiments. The spectra of matrix-isolated model compounds, phenylacetic acid and catechol, were studied under the same experimental conditions. These data were used as references and assisted in the interpretation of the results obtained for DOPAC.

Ultrasensitive and selective detection of dopamine using cobalt-phthalocyanine nanopillar-based surface acoustic wave sensor

A highly selective and sensitive surface acoustic wave (SAW) sensor of dopamine (DA) was developed by depositing cobalt phthalocyanine (CoPc) nanopillars on gold-coated sensing platform of SAW sensor. The developed biosensor presents a sensitivity of 1.6°/nM, has a low limit of detection (LOD) on the order of 0.1 nM, and imparts more selectivity toward DA, since the detection limit of the interfering ascorbic acid (AA) is as high as 1 mM. To understand the selectivity mechanisms of this sensor toward DA, density functional theory-based chemical calculations were carried out. Calculations suggest two different types of interactions: dative bond with a very strong character for DA-CoPc complexes, and significant ionic character in the case of AA-CoPc ones. The interaction energies, in liquid phase, were estimated to be equal to -81 kJ mol(-1) and -38 kJ mol(-1) for DA-CoPc and AA-CoPc complexes, respectively, therefore accounting for the selective detection of DA over AA using tandem CoPc nanopillar-based SAW sensor device. This work demonstrates a simple and efficient design of SAW sensors employing thin nanostructured CoPc biomolecular recognition layers for DA detection.

Competing intramolecular vs. intermolecular hydrogen bonds in solution

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed.

Accurate molecular structure and spectroscopic properties of nucleobases: a combined computational-microwave investigation of 2-thiouracil as a case study

The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier transform microwave spectrometers. The joint experimental-computational study allowed us to determine the accurate molecular structure and spectroscopic properties of the title molecule, but more importantly, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules.

Conformational analysis of octopamine and synephrine in the gas phase

Four and six conformers of the neurotransmitters octopamine and synephrine, respectively, have been identified in the gas phase using a laser ablation device in combination with a molecular-beam Fourier transform microwave spectrometer operating in the 4-10 GHz frequency range. The identification of all of the conformers was based on a comparison of the experimental rotational and (14)N quadrupole coupling constants with those predicted by ab initio calculations, as well as the relative values of their electric dipole moment components. The conformational preferences have been rationalized in terms of the various intramolecular forces operating in the different conformers of the studied molecules. All observed species are characterized by an intramolecular hydrogen bond of the type O-H···N established in the side chain of the neurotransmitters, which adopts an extended disposition in their most stable forms. For conformers with a folded side chain, an extra N-H···π hydrogen-bond-type interaction is established between the amino group and the π system of the aromatic ring.