Dissecting Bonding Interactions in Cysteine Dimers

Neutral (n) and zwitterionic (z) forms of cysteine monomers are combined in this work to extensively explore the potential energy surfaces for the formation of cysteine dimers in aqueous environments represented by a continuum. A simulated annealing search followed by optimization and characterization of the candidate structures afforded a total of 746 structurally different dimers held together via 80 different types of intermolecular contacts in 2894 individual non-covalent interactions as concluded from Natural Bond Orbitals (NBO), Quantum Theory of Atoms in Molecules (QTAIM) and Non-Covalent Interactions (NCI) analyses. This large pool of interaction possibilities includes the traditional primary hydrogen bonds and salt bridges which actually dictate the structures of the dimers, as well as the less common secondary hydrogen bonds, exotic X⋯Y (X = C, N, O, S) contacts, and H⋯H dihydrogen bonds. These interactions are not homogeneous but have rather complex distributions of strengths, interfragment distances and overall stabilities. Judging by their Gibbs bonding energies, most of the structures located here are suitable for experimental detection at room conditions.

Elusive intermediates in cisplatin reaction with target amino acids: Platinum(II)-cysteine complexes assayed by IR ion spectroscopy and DFT calculations

The reactivity of a widely used metal based antineoplastic drug, cisplatin, cis-PtCl₂(NH₃)₂, with L-cysteine (Cys) has been investigated using a combination of electrospray ionization mass spectrometry (ESI-MS), IRMPD gas phase ion spectroscopy and DFT calculations. The cysteine lateral chain represents one of the main platination sites in proteins, which is believed to be related to the resistance mechanisms to cisplatin. The vibrational features of the mass-selected substitution product cis-[PtCl(NH₃)₂(Cys)]⁺ and the intercepted cis-[PtCl(NH₃)₂(H₂O)(Cys)]⁺ intermediate complex were compared to calculated IR spectra, enabling the assessment of the sampled ions structures. In cis-[PtCl(NH₃)₂(Cys)]⁺, cysteine was found to bind platinum through the sulfur atom as a thiolate zwitterion, highlighting the enhanced acidity of the cysteine thiol group upon metal coordination. The cis-[PtCl(NH₃)₂(H₂O)(Cys)]⁺ structure complies with the non-covalent encounter complex, formed by cis-[PtCl(NH₃)₂(H₂O)]⁺ and neutral cysteine. This species is able to undergo the substitution process to produce cis-[PtCl(NH₃)₂(Cys)]⁺ when activated as a mass-isolated ion suggesting its participation in the reaction mechanism of cisplatin with cysteine in solution. Finally, the DFT-calculated energy profile for the substitution reaction was correlated with the peculiar gas-phase reactivity of this non-covalent complex, resulting to be 10-fold less reactive toward substitution than the corresponding methionine complex.

Binding Motifs in the Naked Complexes of Target Amino Acids with an Excerpt of Antitumor Active Biomolecule: An Ion Vibrational Spectroscopy Assay

The structures of proton-bound complexes of 5,7-dimethoxy-4H-chromen-4-one (1) and basic amino acids (AAs), namely, histidine (His) and lysine (Lys), have been examined by means of mass spectrometry coupled with IR ion spectroscopy and quantum chemical calculations. This selection of systems is based on the fact that 1 represents a portion of glabrescione B, a natural small molecule of promising antitumor activity, while His and Lys are protein residues lining the cavity of the alleged receptor binding site. These species are thus a model of the bioactive adduct, although clearly the isolated state of the present study bears little resemblance to the complex biological environment. A common feature of [1+AA+H]⁺ complexes is the presence of a protonated AA bound to neutral 1, in spite of the fact that the gas-phase basicity of 1 is comparable to those of Lys and His. The carbonyl group of 1 acts as a powerful hydrogen-bond acceptor. Within [1+AA+H]⁺ the side-chain substituents (imidazole group for His and terminal amino group for Lys) present comparable basic properties to those of the α-amino group, taking part to a cooperative hydrogen-bond network. Structural assignment, relying on the comparative analysis of the infrared multiple photon dissociation (IRMPD) spectrum and calculated IR spectra for the candidate geometries, derives from an examination over two frequency ranges: 900-1800 and 2900-3700 cm^-1 . Information gained from the latter one proved especially valuable, for example, pointing to the contribution of species characterized by an unperturbed carboxylic OH or imidazole NH stretching mode.

Augmenting Basin-Hopping With Techniques From Unsupervised Machine Learning: Applications in Spectroscopy and Ion Mobility

Evolutionary algorithms such as the basin-hopping (BH) algorithm have proven to be useful for difficult non-linear optimization problems with multiple modalities and variables. Applications of these algorithms range from characterization of molecular states in statistical physics and molecular biology to geometric packing problems. A key feature of BH is the fact that one can generate a coarse-grained mapping of a potential energy surface (PES) in terms of local minima. These results can then be utilized to gain insights into molecular dynamics and thermodynamic properties. Here we describe how one can employ concepts from unsupervised machine learning to augment BH PES searches to more efficiently identify local minima and the transition states connecting them. Specifically, we introduce the concepts of similarity indices, hierarchical clustering, and multidimensional scaling to the BH methodology. These same machine learning techniques can be used as tools for interpreting and rationalizing experimental results from spectroscopic and ion mobility investigations (e.g., spectral assignment, dynamic collision cross sections). We exemplify this in two case studies: (1) assigning the infrared multiple photon dissociation spectrum of the protonated serine dimer and (2) determining the temperature-dependent collision cross-section of protonated alanine tripeptide.

A parallelized molecular collision cross section package with optimized accuracy and efficiency

A new parallelized calculation package predicts collision cross sections with high accuracy and efficiency.

The structures and properties of anionic tryptophan complexes

IRMPD spectroscopy and electronic structure calculations are employed to identify π–π interactions in ionic tryptophan clusters.

Competition between salt bridge and non-zwitterionic structures in deprotonated amino acid dimers

The effect of side chain functional groups on salt bridge structures in deprotonated amino acid homodimers is investigated using both infrared multiple photon dissociation spectroscopy between 650 and 1850 cm⁻¹ and theory.

Interaction of B12F122- with All-cis 1,2,3,4,5,6 Hexafluorocyclohexane in the Gas Phase

Clusters of all-cis 1,2,3,4,5,6-hexafluorocyclohexane and the dodecafluorododecaboron dianion, [C₆F₆H₆]_n[B₁₂F₁₂]^2- (n = 0-4), are investigated in a combined experimental and computational study. DFT calculations and IRMPD spectra in the region of 800-2000 cm^-1 indicate that C₆H₆F₆ binds to open trigonal faces of B₁₂F₁₂^2- via a three-point interlocking binding motif. Calculated binding interactions reveal substantial contributions from C-H···F hydrogen bonding and binding energies that are among the strongest observed for a neutral-anion system.

Intramolecular cation–π interactions in protonated phenylalanine derivatives

The structures and properties of a series of phenylalanine (Phe) derivatives have been investigated in a joint computational and experimental infrared multiple photon dissociation (IRMPD) study.