A matrix isolation study on Ac-Gly–NHMe and Ac-l-Ala–NHMe, the simplest chiral and achiral building blocks of peptides and proteins

After 50 Years of Vibrational Circular Dichroism Spectroscopy: Challenges and Opportunities of Increasingly Accurate and Complex Experiments and Computations

VCD research continues to thrive, driven by ongoing experimental and theoretical advances. Modern studies deal with increasingly complex samples featuring weak intermolecular interactions and shallow potential energy surfaces. Likewise, the combination of VCD measurements with, for instance, cryo-spectroscopic techniques has significantly increased their sensitivity. The extent to which such modern measurements enhance the informative value of VCD depends significantly on the quality of the theoretical models, which must adequately account for anharmonicity, solvation and molecular dynamics. We herein discuss how experimental advancements engage in a stimulating interplay with recent theoretical developments, pursuing either the static or the dynamic computational route. Both paths have their own strengths and limitations, each addressing fundamentally different problems. We give an outlook on future challenges of VCD research, including the possibility to combine static and dynamic approaches to obtain a full picture of the sample.

Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers

Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.

Vibrational Circular Dichroism of a Chiral Triplet Nitrene Investigated Under Matrix-Isolation Conditions in Parahydrogen

Vibrational circular dichroism (VCD) spectra of chiral high-spin organic radicals are expected to show a strong intensity enhancement and are thought to be difficult to predict using state-of-the-art theoretical methods. Herein we show that the chiral triplet nitrene obtained from photochemical cleavage of N2 from enantiopure 2-azido-9H-fluorenol does not feature extraordinarily strong intensities and that the experimental spectra match nicely with calculated ones. Thereby, this study demonstrates the general feasibility of studies on chiral high-spin organics by matrix-isolation VCD.

Hydrocarboxyl Radical as a Product of α-Alanine Ultraviolet Photolysis

UV photodissociation of α-alanine was studied by parahydrogen matrix isolation infrared spectroscopy. The temporal behavior of Fourier transform infrared spectra revealed that UV irradiation at 213 nm yielded the HOCO radical as a direct photoproduct from the S₂ excited state. The concentration of HOCO quickly approached a steady state due to secondary photodissociation of HOCO to produce CO₂ + H or CO + OH. On the other hand, no photoproducts were detected by S₁ excitation at 266 nm. Irradiation of fully deuterated α-alanine at 213 nm yielded ∼2 times more cis-DOCO radicals than the lower energy isomer trans-DOCO, indicating that the conformation of the hydroxyl group is fairly well-preserved upon photodissociation of α-alanine. The present study suggests that HOCO may be a good tracer species in the search for amino acids in interstellar space.

Structural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case

The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)^MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm^-1, has been obtained by combining CCSD(T)/(CBS+CV)^MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.

Application of a transparent window vibrational probe (azido probe) to the structural dynamics of model dipeptides and amyloid β-peptide

The azido asymmetric stretching motion is widely used for the elucidation of the intrinsic conformational preference and folding mechanism of protein since it has strong vibrational absorbance in the spectral transparent windows. However, the possible secondary structural disturbance induced by the insertion of azido group in the side chain of polypeptides should be carefully evaluated. Here, DFT calculation and enhanced sampling method were employed for model dipeptides with or without azido substitution, and the outcome results show that the lower potential energy basins of isolated model dipeptides are consistent with the preferred structural distributions of model dipeptides in aqueous solution. The azido asymmetric stretching frequency shows its sensitivity to the backbone configurations just like amide-I vibration does, and the azido vibration exhibits great potential as a structural reporter in the transparent window. For the evaluation of the application of azido group in biologically related system, the structural dynamics of Aβ_37-42 and N₃-Aβ_37-42 fragments and the self-assemble process of their protofiliments in aqueous solution were demonstrated. The outcome results show that the structural fluctuations of Aβ_37-42 and its protofilament in aqueous solution are quite similar with or without azido substitution, and the dewetting transitions of Aβ_37-42 and N₃-Aβ_37-42 β-sheet layers are both complete within 30 ns and assemble into stable protofilaments. Therefore, the azido asymmetric vibrational motion is a minimally invasive structural probe and would not introduce much disturbance to the structural dynamics of polypeptides.

Correcting the record: the dimers and trimers of trans-N-methylacetamide

Raman jet spectroscopy reveals three N-methylacetamide molecules organizing into a ring structure, previously overlooked in computations.

First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids

We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino acids as well as varied side chain protonation states. Furthermore, we studied amino acids and dipeptides in complex with divalent cations (Ca²⁺, Ba²⁺, Sr²⁺, Cd²⁺, Pb²⁺, and Hg²⁺). The database covers the conformational hierarchies of 280 systems in a wide relative energy range of up to 4 eV (390 kJ/mol), summing up to a total of 45,892 stationary points on the respective potential-energy surfaces. All systems were calculated on equal first-principles footing, applying density-functional theory in the generalized gradient approximation corrected for long-range van der Waals interactions. We show good agreement to available experimental data for gas-phase ion affinities. Our curated data can be utilized, for example, for a wide comparison across chemical space of the building blocks of life, for the parametrization of protein force fields, and for the calculation of reference spectra for biophysical applications.

Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes

The solvation effect on the three dimensional structure and the vibrational feature of alanine dipeptide (ALAD) was evaluated by applying the implicit solvents from polarizable continuum solvent model (PCM) through ab initio calculations, by using molecular dynamic (MD) simulations with explicit solvents, and by combining these two approaches. The implicit solvent induced potential energy fluctuations of ALAD in CHCl3, DMSO and H2O are revealed by means of ab initio calculations, and a global view of conformational and solvation environmental dependence of amide I frequencies is achieved. The results from MD simulations with explicit solvents show that ALAD trends to form PPII, αL, αR, and C5 in water, PPII and C5 in DMSO, and C5 in CHCl3, ordered by population, and the demonstration of the solvated structure, the solute-solvent interaction and hydrogen bonding is therefore enhanced. Representative ALAD-solvent clusters were sampled from MD trajectories and undergone ab initio calculations. The explicit solvents reveal the hydrogen bonding between ALAD and solvents, and the correlation between amide I frequencies and the CO bond length is built. The implicit solvents applied to the ALAD-solvent clusters further compensate the solvation effect from the bulk, and thus enlarge the degree of structural distortion and the amide I frequency red shift. The combination of explicit solvent in the first hydration shell and implicit solvent in the bulk is helpful for our understanding about the conformational fluctuation of solvated polypeptides through vibrational probes.

Interfacial water at the trialanine hydrophilic surface: a DFT electronic structure and bottom-up investigation

A model describing a network of hydrogen bonded water-trialanine has been developed to estimate hydration effects on various conformers of the peptide.

Estimation of the rotamerization constants of different conformations of N-acetylalanine: a theoretical and matrix-isolation FT-IR study

The conformational landscape of N-acetylalanine has been investigated by a theoretical and matrix-isolation FT-IR study. Optimizations of N-acetylalanine structures has been conducted at successive higher levels of theory HF/3-21G, DFT(B3LYP)/6-31++G** and MP2/6-31++G**. This resulted in three stable conformations. Among these, one conformation contains an intramolecular H-bond. The vibrational properties of these conformations were calculated and used to identify the conformations in a cryogenic argon matrix. The intensities of some bands assigned to a particular conformation were used to estimate the rotamerization constants K(r12) and K(r13) for the equilibria NAA1 NAA2 and NAA1 NAA3, respectively. The obtained experimental values were in agreement with the theoretical predictions.

CONFORMATIONAL PREFERENCES OF N-ACETYL–GLYCINE–GLYCINE–N′-METHYLAMIDE: A THEORETICAL STUDY

The conformational preferences of peptide models have been investigated to understand the protein folding mechanism and to develop the force field. Here, we report the minimum energy conformations for a model peptide, N-acetyl–glycine–glycine–N′-methylamide ( Ac–1Gly–2Gly–NHMe(I) ) at the HF/3-21G, HF/6-31G*, and the B3LYP/6-31G* level of theory. At the B3LYP/6-31G* level, the 31 minima were identified and the 10 β-turn structures among the minima were observed in gas-phase. The conformational preferences of Gly residue in the model peptide, I depend on its relative position and conformation of neighboring Gly residue. The Gly residue in this model dipeptide has an asymmetric energy profile as one of Gly residue adopts a specific conformation. This study sheds some lights on understanding the unique conformational preferences of Gly residue in protein including two consecutive Gly residues.

Gas-phase and Ar-matrix SQM scaling factors for various DFT functionals with basis sets including polarization and diffuse functions

Scaling factors for Pulay's scaled quantum mechanical (SQM) scheme have been determined for four different widely used DFT functionals (PBE, B3LYP, B3PW91, and M06-2X) and for two basis sets (6-31++G** and aug-cc-pVTZ) by fitting computed results to 347 fundamental experimental vibrational frequencies of 33 molecules. Measurements in the gas phase and in solid argon matrices were used independently in the fitting procedure in order to provide a simple method of estimating matrix shifts. The accuracy of the new scaling factors is demonstrated on test molecules including hydrogen-bonded systems and molecules containing chlorine and sulfur atoms.

The stability of Cα peptide radicals: why glycyl radical enzymes?

The conformational space of dipeptide models derived from glycine, alanine, phenylalanine, proline, tyrosine, and cysteine has been searched extensively and compared with the corresponding C(α) dipeptide radicals at the G3(MP2)-RAD level of theory. The results indicate that the (least-substituted) glycine dipeptide radical is the thermochemically most stable of these species. Analysis of the structural parameters indicates that this is due to repulsive interactions between the C(α) substituents and peptide units in the radical. A comparison of the conformational preferences of dipeptide radicals and their closed-shell parents also indicates that radical stability is a strongly conformation-dependent property.

Vibrational circular dichroism spectroscopy of chiral molecules

In this chapter, new developments and main applications of vibrational circular dichroism (VCD) spectroscopy reported in the last 5 years are described. This includes the determinations of absolute configurations of chiral molecules, understanding solvent effects and modeling solvent-solute explicit hydrogen bonding networks using induced solvent chirality, studies of transition metal complexes and their peculiar and enormous intensity enhancements in VCD spectra, investigations of conformational preference of chiral ligands bound to gold nano particles, and two new advances in applying matrix isolation VCD spectroscopy to flexible, multi-conformational chiral molecules and complexes, and in development of femtosecond laser based VCD instruments for transient VCD monitoring. A brief review of the experimental techniques and theoretical methods is also given. The purpose of this chapter is to provide an up-to-date perspective on the capability of VCD to solve significant problems about chiral molecules in solution, in thin film states, or on surfaces.

Alanine polypeptide structural fingerprints at room temperature: what can be gained from non-harmonic Car-Parrinello molecular dynamics simulations

Structural infrared fingerprints of neutral gas phase alanine peptides of increasing size and complexity (dipeptide, octapeptide, and beta-strand peptide) are characterized through DFT-based Car-Parrinello molecular dynamics simulations. Harmonic and nonharmonic vibrational signatures are calculated from the time correlation of the dipole moment of the gas phase peptide in a direct way (without any approximation) respectively from low temperature (20 K) and room temperature (300 K) molecular dynamics. Our main purpose is to answer the two following questions: (i) Is the direct inclusion of temperature for the calculation of infrared spectra mandatory for the comprehension of the vibrational signatures experimentally recorded at room temperature? (ii) To what extent is the amide I, II, and III domain sensitive enough to the local structure of the peptides, to provide vibrational signatures that can be definitely used to assess the peptide conformation at 300 K?