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Register a new userFirst-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids
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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 an overall 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.
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In several previous works, I presented the mirror symmetry in the set of protein amino acids, expressed through the number of atoms. Here, however, the same thing is shown but over the number of nucleons and molecules mass. Compared to the previous version of the paper, minimal changes have been made, and Display 2 as well as Figures 3 and 4 have been added.
The correlations of primary and secondary structures were analyzed using proteins with known structure from Protein Data Bank. The correlation values of amino acid type and the eight secondary structure types at distant position were calculated for distances between -25 and 25. Shapes of the diagrams indicate that amino acids polarity and capability for hydrogen bonding have influence on the secondary structure at some distances. Clear preference of most of the amino acids towards certain secondary structure type classifies amino acids into four groups: alpha-helix admirers, strand admirers, turn and bend admirers and the others. Group four consists of His and Cis, the amino acids that do not show clear preference for any secondary structure. Amino acids from a group have similar physicochemical properties, and the same structural characteristics. The results suggest that amino acid preference for secondary structure type is based on the structural characteristics at Cb and Cg atoms of amino acid. alpha-helix admirers do not have polar heteroatoms on Cb and Cg atoms, nor branching or aromatic group on Cb atom. Amino acids that have aromatic groups or branching on Cb atom are strand admirers. Turn and bend admirers have polar heteroatom on Cb or Cg atoms or do not have Cb atom at all. Our results indicate that polarity and capability for hydrogen bonding have influence on the secondary structure at some distance, and that amino acid preference for secondary structure is caused by structural properties at Cb or Cg atoms.
A gas-phase optical spectrum of a large polycyclic aromatic hydrocarbon (PAH) cation - C78H26 +- in the 410-610 nm range is presented. This large all-benzenoid PAH should be large enough to be stable with respect to photodissociation in the harsh conditions prevailing in the interstellar medium (ISM). The spectrum is obtained via multi-photon dissociation (MPD) spectroscopy of cationic C78H26 stored in the Fourier Transform Ion Cyclotron Resonance (FT-ICR) cell using the radiation from a mid-band optical parametric oscillator (OPO) laser. The experimental spectrum shows two main absorption peaks at 431 nm and 516 nm, in good agreement with a theoretical spectrum computed via time-dependent density functional theory (TD-DFT). DFT calculations indicate that the equilibrium geometry, with the absolute minimum energy, is of lowered, nonplanar C2 symmetry instead of the more symmetric planar D2h symmetry that is usually the minimum for similar PAHs of smaller size. This kind of slightly broken symmetry could produce some of the fine structure observed in some diffuse interstellar bands (DIBs). It can also favor the folding of C78H26 + fragments and ultimately theformation of fullerenes. This study opens up the possibility to identify the most promising candidates for DIBs amongst large cationic PAHs.
X-ray free-electron lasers (XFELs) promise the diffractive imaging of single molecules and nanoparticles with atomic spatial resolution. This relies on the averaging of millions of diffraction patterns of identical particles, which should ideally be isolated in the gas phase and preserved in their native structure. Here, we demonstrated that polystyrene nanospheres and Cydia pomonella granulovirus can be transferred into the gas phase, isolated, and very quickly shockfrozen, i.e. cooled to 4~K within microseconds in a helium-buffer-gas cell, much faster than state-of-the-art approaches. Nanoparticle beams emerging from the cell were characterized using particle-localization microscopy with light-sheet illumination, which allowed for the full reconstruction of the particle beams, focused to $<100:mutext{m}$, as well as for the determination of particle flux and number density. The experimental results were quantitatively reproduced and rationalized through particle-trajectory simulations. We propose an optimized setup with cooling rates for few-nanometers particles on nanoseconds timescales. The produced beams of shockfrozen isolated nanoparticles provide a breakthrough in sample delivery, e.g. for diffractive imaging and microscopy or low-temperature nanoscience.
This paper presents, for the first time, four diversity types of protein amino acids. The first type includes two amino acids (G, P), both without standard hydrocarbon side chains; the second one four amino acids, as two pairs [(A, L), (V, I)], all with standard hydrocarbon side chains; the third type comprises the six amino acids, as three pairs [(F, Y), (H, W), (C, M)], two aromatic, two hetero aromatic and two hetero non-aromatic); finally, the fourth type consists of eight amino acids, as four pairs [(S, T), (D, E), (N, Q), (K, R)], all with a functional group which also exists in amino acid functional group (wholly presented: H2N-.CH-COOH; separately: OH, COOH, CONH2, NH2). The insight into existence of four types of diversity was possible only after an insight into the existence of some very new arithmetical regularities, which were so far unknown. Also, as for showing these four types was necessary to reveal the relationships between several key harmonic structures of the genetic code (which we presented in our previous works), this paper is also a review article of the authors researches of the genetic code. By this, the review itself shows that the said harmonic structures are connected through the same (or near the same) chemically determined amino acid pairs, 10 pairs out of the 190 possible.
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