Prediction of protein pKa with representation learning

The behavior of proteins is closely related to the protonation states of the residues. Therefore, prediction and measurement of pK_a are essential to understand the basic functions of proteins. In this work, we develop a new empirical scheme for protein pK_a prediction that is based on deep representation learning. It combines machine learning with atomic environment vector (AEV) and learned quantum mechanical representation from ANI-2x neural network potential (J. Chem. Theory Comput. 2020, 16, 4192). The scheme requires only the coordinate information of a protein as the input and separately estimates the pK_a for all five titratable amino acid types. The accuracy of the approach was analyzed with both cross-validation and an external test set of proteins. Obtained results were compared with the widely used empirical approach PROPKA. The new empirical model provides accuracy with MAEs below 0.5 for all amino acid types. It surpasses the accuracy of PROPKA and performs significantly better than the null model. Our model is also sensitive to the local conformational changes and molecular interactions.

We developed new empirical ML model for protein pK_a prediction with MAEs below 0.5 for all amino acid types.     

Polarization control and sensing with two-dimensional coupled photonic crystal microcavity arrays

We have experimentally studied polarization properties of the two-dimensional coupled photonic crystal microcavity arrays and observed a strong polarization dependence of the transmission and reflection of light from the structures-effects that can be employed in building miniaturized polarizing optical components. Moreover, by combining these properties with a strong sensitivity of the coupled bands on the surrounding refractive index, we have demonstrated a detection of small refractive-index changes in the environment, which is useful for construction of biochemical sensors.     

The effect of nitrogen atom on double bond pyramidalization

The title compound 6-phenyl-4,6,8-triazatetracyclo[9.2.1.0^2,10.0^4,8]tetradec-2(10)-ene-5,7-dione (6) has been synthesized by the addition of 4-phenyl-1,2,4-triazole-3,5-dione (PTAD) to 2,3-dimethylenebicyclo[2.2.1]heptane. The cell parameters are a = 9.991(5), b = 11.754(9), c = 6.549(5) Å, = 101.08(7)°, = 103.31(5)°, = 98.24(5)°. The crystal structure of 6 was determined. The obtained geometrical parameters were highly correlated with the DFT calculations. The experimentally determined folding angle of the double bond was found to be 8.44°. The effect of the electron-withdrawing ability of nitrogen atom on the degree of pyramidalization is discussed.     

Synthesis and Spectral and Electrochemical Characterization of Novel Substituted 1,4-Naphthoquinone Derivatives

The novel substituted 2,3-dichloro-1,4-naphthoquinone derivatives were synthesized from the reactions of (1) and related nucleophilles in sodium carbonate (Na₂CO₃) solution of ethanol, chloroform with Et₃N, or potassium carbonate (K₂CO₃) solution of acetonitrile. The structures of novel compounds were characterized by using microanalysis, Fourier transform–infrared, ¹H NMR, ¹³C NMR, mass spectrometry, and cyclic voltammetry (CV).

[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource(s): Full experimental and spectral details.]     

Cellulose/cysteine based thiol-ene UV cured adsorbent: removal of silver (I) ions from aqueous solution

Cellulose - In the present study, a novel, eco-friendly, and simple polymeric adsorbent was obtained from cellulose acetate butyrate (CAB) and cysteine (Cys) to remove silver (I) ions in the...     

Contemporary Photoligation Chemistry: The Visible Light Challenge

Catalyst-free and bond-forming light-induced reactions have seen an unprecedented renaissance in the realm of soft matter materials science due to their efficiency, spatio-temporal controllability and, sometimes, photoreversible nature. However, many of these reactions rely on the application of high energy UV light that can cause photo-degradation and is inapplicable in biological environments. If up-conversion systems or two-photon processes are to be avoided, strategies for red-shifting catalyst-free ligation technology are critically required. This Concept article introduces the reader to recent methods that lead to efficient, catalyst-free visible-light-induced ligation chemistry based on polyaromatic substituted photoreactive compounds—pyrene and anthracene—and, furthermore, emphasizes the broad and facile applicability of these molecules in polymeric material design. Concomitantly, we highlight that a careful action plot analysis of photochemical reactivity can provide deep insights into reactivity patterns, far beyond those suggested by the absorption spectrum. Indeed, we suggest that an action plot analysis is necessary for the evaluation of any photochemical system and its response to structural chemical changes.     

Convergence in Variation for Bernstein-Type Operators

In this paper, we deal with Bernstein-type operators defined by Cárdenas-Morales et al. as \({B_{n}(f \circ \tau^{-1}) \circ \tau}\), where \({B_{n}}\) is the nth Bernstein polynomial (Comput Math Appl 62(1):158–163, 2011). Assuming that \({\tau}\) and f are absolutely continuous functions on \({[0, 1]}\) and inf \({\tau ^{\prime} (x) \geq m > 0}\) as well as \({\tau (0) = 0}\) and \({\tau (1) = 1,}\) we study the convergence of Bernstein-type operators to f in variation seminorm. Moreover, we give a Voronovskaja-type formula and a Jackson-type estimate in the sense of Bardaro et al. (Analysis 23:299–340, 2003).     

Theoretical study on HF elimination and aromatization mechanisms: a case of pyridoxal 5' phosphate-dependent enzyme

Pyridoxal 5-phosphate (PLP), the phosphorylated and the oxidized form of vitamin B6 is an organic cofactor. PLP forms a Schiff base with the ?-amino group of a lysine residue of PLP-dependent enzymes. γ-Aminobutyric acid (GABA) aminotransferase is a PLP-dependent enzyme that degrades GABA to succinic semialdehyde, while reduction of GABA concentration in the brain causes convolution besides several neurological diseases. The fluorine-containing substrate analogues for the inactivation of the GABA-AT are synthesized extensively in cases where the inactivation mechanisms involve HF elimination. Although two proposed mechanisms are present for the HF elimination, the details of the base-induced HF elimination are not well identified. In this density functional theory (DFT) study, fluorine-containing substrate analogue, 5-amino-2-fluorocyclohex-3-enecarboxylic acid, is particularly chosen in order to explain the details of the HF elimination reactions. On the other hand, the experimental studies revealed that aromatization competes with Michael addition mechanism in the presence of 5-amino-2-fluorocyclohex-3-enecarboxylic acid. The results allowed us to draw a conclusion for the nature of HF elimination, besides the elucidation of the mechanism preference for the inactivation mechanism. Furthermore, the solvent phase calculations carried out in this study ensure that the proton transfer steps should be assisted either by a water molecule or a base for lower activation energy barriers.     

Explicit formulas for Hecke Gauss sums in quadratic number fields

We derive an explicit formula for Hecke Gauss sums of quadratic number fields. As an immediate consequence we obtain a quadratic reciprocity law in quadratic number fields which generalizes the classical one given by Hecke. The proofs use, apart from the well-known formulas for ordinary Gauss sums, only elementary algebraic manipulations.