Evaluation of MP2, DFT, and DFT-D Methods for the Prediction of Infrared Spectra of Peptides

Carbon-Rich Plasma-Deposited Silicon Oxycarbonitride Films Derived from 4-(Trimethylsilyl)morpholine as a Novel Single-Source Precursor

4-(trimethylsilyl)morpholine O(CH2CH2)2NSi(CH3)3 (TMSM) was investigated as a single-source precursor for SiCNO films synthesis. Optical emission spectroscopy of plasma generated from TMSM/He, TMSM/H2, and TMSM/NH3 gas mixtures revealed the presence of N2, CH, H, CN, and CO species. The last two are suggested to be responsible for the lowering of carbon concentration in the films in comparison with the precursor. The refractive index ranged from 1.5 to 2.0, and bandgap varied from 2.0 to 4.6 eV, which pointed that some of the films can be used as antireflective coatings in silicon photovoltaic cell technologies and dielectric layers in electronic devices.

Predicting Infrared Spectra with Message Passing Neural Networks

Infrared (IR) spectroscopy remains an important tool for chemical characterization and identification. Chemprop-IR has been developed as a software package for the prediction of IR spectra through the use of machine learning. This work serves the dual purpose of providing a trained general-purpose model for the prediction of IR spectra with ease and providing the Chemprop-IR software framework for the training of new models. In Chemprop-IR, molecules are encoded using a directed message passing neural network, allowing for molecule latent representations to be learned and optimized for the task of spectral predictions. Model training incorporates spectra metrics and normalization techniques that offer better performance with spectral predictions than standard practice in regression models. The model makes use of pretraining using quantum chemistry calculations and ensembling of multiple submodels to improve generalizability and performance. The spectral predictions that result are of high quality, showing capability to capture the extreme diversity of spectral forms over chemical space and represent complex peak structures.

Conformational analysis by UV spectroscopy: the decisive contribution of environment-induced electronic Stark effects

UV chromophores are frequently used as probes of the molecular structure. In particular, they are sensitive to the electric field generated by the molecular environment, resulting in the observation of Stark effects on UV spectra. While these environment-induced electronic Stark effects (EI-ESE) are already used for conformational analysis in the condensed phase, this work explores the potential of such an approach when performed at much higher conformational resolution in the gas phase. By investigating model alkali benzylacetate and 4-phenylbutyrate ion pairs, where the electric field applied to the phenyl ring is chemically tuned by changing the nature of the alkali cation, this work demonstrates that precise conformational assignments can be proposed based on the correlation between the conformation-dependent calculated electric fields and the frequency of the electronic transitions observed in the experimental UV spectra. Remarkably, the sole analysis of Stark effects and fragmentation patterns in mass-selected UV spectra provided an accurate and complete conformational analysis, where spectral differences as small as a few cm-1 between electronic transitions were rationalized. This case study illustrates that the identification of EI-ESE together with their interpretation at the modest cost of a ground state electric field calculation qualify UV spectroscopy as a powerful tool for conformational analysis.

Investigation of nanotubes as the smart carriers for targeted delivery of mercaptopurine anticancer drug

Mercaptopurine (MCP) is an anticancer drug that is used to treat acute lymphoblastic leukemia. The therapeutic effect of the mercaptopurine limits its severe side effects like other cytotoxic (anti-cancer) drugs. Nanostructures or nanoparticles can be widely used as potential drug carriers for diagnosis and treatment of cancer. In the current study, the boron nitride nanotube (BNNT) and carbon nanotube (CNT) were studied as the delivery carriers of MCP using the density functional theory (DFT) calculations and molecular dynamics (MDs) simulation studies. To further understand the electronic properties of mercaptopurine, the partial density of states (PDOS) was calculated. The PDOS results depicted that the electronic features of the MCP do not change after the adsorption on the surface of the nanotubes. More stability of the MCP/BNNT complexes may be attributed to the existence of the intermolecular hydrogen bonds (H-bonds) between the hydrogen atoms of the MCP molecule and the N atoms of the BNNT. The results of the quantum theory of atoms in molecules (QTAIM) confirmed the presence of H-bonds in these complexes. Moreover, MD simulation studies were done in the presence of five drug molecules. The results revealed that the strongest van der Waals (vdW) interaction energy was found between the BNNT and MCP among the studied nanotubes, indicating the BNNT is a better nanocarrier than carbon nanotube for delivery of the MCP drug within the biological systems. In general, the obtained results may present helpful information on the nature of the interactions between mercaptopurine anticancer drug with BNNT and/or CNT.Communicated by Ramaswamy H. Sarma.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.

A combined molecular dynamics simulation and quantum mechanics study on mercaptopurine interaction with the cucurbit [6,7] urils: Analysis of electronic structure

In the current study, the probability of complex formation between mercaptopurine drug with cucurbit[6]urils and cucurbit[7]urils has been investigated. The calculations for geometry optimization of complexes have been carried out by means of DFT (B3LYP), DFT-D (B3LYP-D) and M06-2X methods. The Atoms In Molecules (AIM), Natural Bond Orbital (NBO), NMR, the density of states (DOSs) and frontier molecular orbital (MO) analyses have been done on the inclusion complexes. In addition, the UV-Vis spectra of the first eight states have been obtained by CAM-B3LYP/TD-DFT calculation. The obtained results of the complexation process reveal that CB[7]-DRG complexes are more favorable than that of CB[6]-DRG interactions. Furthermore, our theoretical results show that configurations III and I are the most stable configurations related to the CB[6]/DRG and CB[7]/DRG interactions, respectively. The positive ∇²_ρ(r) and HC values at the bond critical points indicate that exist the weak H-bonds between CB[6] and CB[7] with H atoms of the drug molecule. The obtained negative binding energy values of CB[7]-DRG interaction in solution phase show the stability of these complexes in the aqueous medium. Also, all of the observed parameters of molecular dynamics simulation such as the number of contacts, hydrogen bonding, center-of-mass distance and van der Waals energy values confirm the encapsulation of mercaptopurine molecule inside the cucurbit[7]urils cavity at about 3.2ns.

Structural analyses of isolated cyclic tetrapeptides with varying amino acid residues

Structural analyses of isolated cyclic tetrapeptides with varying amino acid residues were performed by applying combined IR/UV spectroscopy in the molecular beam and DFT calculations. The intrinsic structural properties especially with regard to the influence of different amino acid residues are fundamental for optimizing their binding ability.

Computational insights into the molecular interaction and ion-pair structures of a novel zinc-functionalized ionic liquid, [Emim][Zn(TFSI)₃]

The ion pair structures of a novel CO2 capture material in the form of a metal chelate anion-containing room temperature ionic liquid (IL), 1-ethyl-3-methylimidazolium tri[bis(trifluoromethylsulfonyl)imide]zincate(II), [Emim][Zn(TFSI)3], were elucidated by correlating the infrared spectra generated using density functional theory (DFT) calculations with the experimental spectrum derived from a room temperature infrared spectroscopic measurement. A free volume energy minimization algorithm revealed stable structures where the zinc ion forms an octahedral, homoleptic complex with the ligand bis(trifluoromethylsulfonyl)imide through coordination with the oxygen of the sulfone group, with 1-ethyl-3-methylimidazolium acting as the counterion. The method of analysis was built around 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [Emim][TFSI], involving direct comparison with published data, and extended to the more complex [Emim][Zn(TFSI)3] system. The DFT calculations reproduced the vibrational spectra of [Emim][Zn(TFSI)3] and [Emim][TFSI] using their optimized geometries, with correlation slopes of 0.9996 and 1.0022, respectively. Comparison of the vibrational modes of [Emim][TFSI] and [Emim][Zn(TFSI)3] provided insights into the ion pair structure of, and molecular interactions in the ILs analyzed.

Structural investigations on a linear isolated depsipeptide: the importance of dispersion interactions

The first molecular beam investigations of an isolated linear depsipeptide are presented. By applying IR/UV spectroscopic methods and DFT calculations three structural arrangements are identified with the most stable structure being only stable by including dispersion interactions.

Isolated neutral peptides

This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.

Effects of the basis set and of the exchange-correlation functional on the Inelastic Electron Tunneling signatures of 1,4-benzenedithiol

The effects of the atomic basis set and of the exchange-correlation (XC) functional on the Inelastic Electron Tunneling (IET) spectra have been investigated by considering the prototypical 1,4-benzenedithiol molecule. These studies have been completed by tackling the reliability of the same methods for predicting the IR absorption spectrum of the same molecule. The main conclusions are (i) the B3LYP XC functional is suitable to predict the relative vibrational frequencies, (ii) provided a scaling factor is used, the root mean square error on the vibrational frequencies goes down to 18 cm(-1), (iii) triple-ζ basis sets and in particular the cc-pVTZ basis set is a good compromise between accuracy and computational needs, (iv) basis set effects on the IET intensities are larger than those of the XC functional, and (v) the cc-pVTZ, cc-pVQZ, and aug-cc-pVDZ basis sets provide consistent IET intensities.

Isolated monohydrates of a model peptide chain: effect of a first water molecule on the secondary structure of a capped phenylalanine

The formation of monohydrates of capped phenylalanine model peptides, CH(3)-CO-Phe-NH(2) and CH(3)-CO-Phe-NH-CH(3), in a supersonic expansion has been investigated using laser spectroscopy and quantum chemistry methods. Conformational distributions of the monohydrates have been revealed by IR/UV double-resonance spectroscopy and their structures assigned by comparison with DFT-D calculations. A careful analysis of the final hydrate distribution together with a detailed theoretical investigation of the potential energy surface of the monohydrates demonstrates that solvation occurs from the conformational distribution of the isolated peptide monomers. The distribution of the monohydrates appears to be strongly dependent on both the initial monomer conformation (extended or folded backbone) and the solvation site initially occupied by the water molecule. The solvation processes taking place during the cooling can be categorized as follows: (a) solvation without significant structural changes of the peptide, (b) solvation inducing significant distortions of the backbone but retaining the secondary structure, and (c) solvation triggering backbone isomerizations, leading to a modification of the peptide secondary structure. It is observed that solvation by a single water molecule can fold a β-strand into a γ-turn structure (type c) or induce a significant opening of a γ-turn characterized by an elongated C(7) hydrogen bond (type b). These structural changes can be considered as a first step toward the polyproline II condensed-phase structure, illustrating the role played by the very first water molecule in the solvation process.

Experimental and theoretical investigation of the aromatic-aromatic interaction in isolated capped dipeptides

Among the forces responsible for shaping proteins, interactions between side chains of aromatic residues play an important role as they are involved in the secondary and the tertiary structures of proteins contributing to the formation of hydrophobic domains. The purpose of this paper is to document this interaction in two capped dipeptides modeling a segment of a protein chain having two consecutive Phe residues, Ac-Phe-Phe-NH(2) and Ac-Phe-D-Phe-NH(2). These two molecules have been investigated in the gas phase by IR/UV double resonance spectroscopy, and the assignment of the observed conformers has been done by comparison with quantum chemistry calculations. Both peptides are found to adopt a beta-turn type I conformation stabilized by an edge-to-face interaction between the two aromatic rings. Comparison with other dipeptides in the literature demonstrates the impact of this aromatic-aromatic interaction on the shape adopted by the peptide chain, and its role among the other shaping forces (H-bonds, NH-pi interactions) is discussed. As an illustration, the H-bond strength is found to be significantly lower in the beta-turn type I conformer, in which the two rings interact, as compared to the similar conformer where such an interaction does not exist. This structural feature due to the backbone distortion induced by the interaction between the aromatic rings makes this system a good test for evaluating the ability of computational methods to correctly account for the competition between these forces. MP2, SCS-MP2, DFT, and DFT-D methods have been assessed in this respect. Comparison between geometries, energies, and frequency calculations illustrate their respective limitations in describing conformations resulting from a subtle equilibrium between the several interactions at play.

Structure of sodiated octa-glycine: IRMPD spectroscopy and molecular modeling

The structure of the sodiated peptide GGGGGGGG-Na(+) or G(8)-Na(+) was investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and a combination of theoretical methods. IRMPD was carried out in both the fingerprint and N-H/O-H stretching regions. Modeling used the polarizable force field AMOEBA in conjunction with the replica-exchange molecular dynamics (REMD) method, allowing an efficient exploration of the potential energy surface. Geometries and energetics were further refined at B3LYP-D and MP2 quantum chemical levels. The IRMPD spectra indicate that there is no free C-terminus OH and that several N-Hs are free of hydrogen bonding, while several others are bound, however not very strongly. The structure must then be either of the charge solvation (CS) type with a hydrogen-bound acidic OH, or a salt bridge (SB). Extensive REMD searches generated several low-energy structures of both types. The most stable structures of each type are computed to be very close in energy. The computed energy barrier separating these structures is small enough that G(8)-Na(+) is likely fluxional with easy proton transfer between the two peptide termini. There is, however, good agreement between experiment and computations in the entire spectral range for the CS isomer only, which thus appears to be the most likely structure of G(8)-Na(+) at room temperature.

Investigations of the water clusters of the protected amino acid Ac-Phe-OMe by applying IR/UV double resonance spectroscopy: microsolvation of the backbone

In order to investigate the influence of hydration on the backbone of a peptide or protected amino acid, the successive aggregation of water to Ac-Phe-OMe is analysed by means of IR/UV double resonance spectroscopy. To achieve meaningful results the spectra have been recorded in the region of the amide A and OH stretching vibrations as well as the amide I/II modes. Comparison with ab initio and DFT calculations leads to size-selective structural assignments. Two isomers of the mono- and dihydrated clusters and one isomer of the trihydrated cluster are observed in the molecular beam leading to a formation of the first solvation shell of the backbone. In case of the trihydrated cluster the backbone geometry is remarkably changed compared to the structure of the monomer since a network of water molecules can be formed.