Accurate Estimation of pKb Values for Amino Groups from Surface Electrostatic Potential (VS,min) Calculations: The Isoelectric Points of Amino Acids as a Case Study

DensToolKit2: A comprehensive open-source package for analyzing the electron density and its derivative scalar and vector fields

In this article, we provide details of the suite DensToolKit-v2, which consists of a set of cross-platform, optionally parallelized programs for analyzing the molecular electron density (ρ), as well as different fields and chemical indices derived from it. Notably, with this version, the user can compute the Non-Covalent Interaction index, the Density Overlap Regions Index, and fields related to single-spin-type molecular orbitals, such as the spin density. In addition, DensToolKit-v2 includes several programs for analyzing other less-known fields, such as the Density Matrix of order 1, the two-electron pair density function, and the Fourier transforms of these fields, that is, functionals in momentum space. A new sub-program to compute integrated properties of each of the fields released in the suite is included. A simple graphical user interface is released, which eases the visualization of ρ critical points topology. Most interestingly, this version includes a program that renders estimations of pKa's of carboxylic acids and pKb's of amines (primary, secondary, and tertiary) through refined relations between experimental data and the molecular electrostatic potential computed at isosurfaces of ρ. Details related to the speed of the programs and a few examples of how to use the program in workflows are discussed, and the source code is released through a git repository under the GPLv3 terms.

Globin ferryl species: what is the nature of the protonation event at pH < 5?

The ferryl state in globins has previously been reported to undergo a protonation event below pH 5, as assessed using pH jump experiments with stopped-flow UV-Vis spectroscopy. This protonation entails hypsochromic shifts in the α and β bands (~ 20 to 40 nm) and an ~ 10 nm reduction in the energy difference between these two bands. We now report that in Mb this event is also characterized by a hypsochromic shift in the Soret band (~ 5 nm). No similar shifts in Soret, α, and β bands are seen upon the denaturation of ferryl Mb with guanidine-suggesting that the spectroscopic changes in ferryl Mb at pH < 5 are not caused by changes in the solvent exposure or in hydrogen bonding around the ferryl unit. Under the same denaturing conditions (pH jump below pH 5, and/or guanidine), ferric-aqua and ferrous-oxy Mb show no spectral changes of the order seen in the ferryl pH jump experiments. Together, these observations suggest that the protonation event is localized on the iron-bound oxygen atom, as opposed to somewhere on a hydrogen-bonding partner. Time-dependent density functional theory (TD-DFT) calculations were not able to systematically predict the UV-Vis spectra of the heme to the level of detail needed to interpret the experimental findings in this study.

Theoretical Investigation on Proton Transfer Directionality and Dynamics Behavior of 3-(Benzo[d]thiazol-2-yl)-2-hydroxy-5-methoxybenzaldehyde with Two Asymmetric Proton Acceptors

A detailed theoretical investigation on the excited state intramolecular proton transfer (ESIPT) directionality and dynamics behavior of 3-(benzo[d]thiazol-2-yl)-2-hydroxy-5-methoxybenzaldehyde (BTHMB) with two unsymmetric proton acceptors (N and O2) has been performed. The hydrogen bond O1-H···N in BTHMB-a formed by the O1-H group with the N atom or O1-H···O2 in BTHMB-b formed by the O1-H group with the O2 atom is enhanced upon photoexcitation, and the strength of the O1-H···N bond is stronger, which will drive the O1-H proton to the N atom. Potential energy curves further confirm that ESIPT occurs in the N atom because of the smaller energy barrier (0.39 kcal/mol). Results of dynamics simulations manifest that no surface hopping exists between the S0 and S1 states within 300 fs, and ESIPT time constants of BTHMB-a and BTHMB-b are 48 and 151 fs, respectively. While the reverse ESIPT is observed in BTHMB-b at 294 fs, implying that the O1-H proton is transferred to the N atom instead of the O2 atom. The consistency of the calculated absorption (390 nm) and fluorescence spectra (443 and 602 nm) of BTHMB-a with the experimental values (390, 410, and 605 nm) confirms this conclusion again. The charge distribution analysis shows that the charge on the proton acceptors increases, and the O2 atom has higher electronegativity because it has more negative charges. The minimum surface electrostatic potential on the N atom in BTHMB-b correlating with the pKb value is -47.38 kcal/mol, indicating that the N atom has strong basicity. Therefore, the basicity of the N atom dominates the ESIPT process rather than the electronegativity of the O2 atom.

Elucidating Mechanism and Selectivity in Pyridine Functionalization Through Silylium Catalysis

The functionalization of aromatic N-heterocycles through silylium activation demonstrates exceptional selectivity and efficiency. Density functional theory (DFT) calculations unveil the detailed silylium catalysis mechanism and elucidate the origins of selectivity in this reaction. The phosphoramidimidate sulfonamide (PADI) precatalyst orchestrates of the catalytic cycle via three elementary steps. The Brønsted acidity of precatalyst significantly influences both the formation of silylium-based Lewis acid active species and the silylium activation of pyridine. Unlike disulfonimide (DSI)-type precatalysts, both Tf2NH and PADI precatalysts with strong acidities can easily promote the generation of activated silylium pyridine species. A semi-enclosed 'rigid' electronegative cavity in PADI-type anions constructs a well-defined recognition site, facilitating engagement with the positively charged silylium pyridine species. Due to the high electrophilicity and less steric demand at the C4-position of the pyridine substrate, the product with C4-regioselectivity was predominantly generated.

Synergistic Buried Interface Regulation of Tin-Lead Perovskite Solar Cells via Co-Self-Assembled Monolayers

Tin-lead (Sn-Pb) perovskite solar cells (PSCs) hold considerable potential for achieving efficiencies near the Shockley-Queisser (S-Q) limit. Notably, the inverted structure stands as the preferred fabrication method for the most efficient Sn-Pb PSCs. In this regard, it is imperative to implement a strategic customization of the hole selective layer to facilitate carrier extraction and refine the quality of perovskite films, which requires effective hole selectivity and favorable interactions with Sn-Pb perovskites. Herein, we propose the development of Co-Self-Assembled Monolayers (Co-SAM) by integrating both [2-(9H-carbazol-9-yl)ethyl]phosphonic acid (2PACz) and glycine at the buried contacts. The one-step deposition process employed in the fabrication of the Co-SAM ensures uniform coverage, resulting in a homogeneous surface potential. This is attributed to the molecular interactions occurring between 2PACz and glycine in the processing solution. Furthermore, the amine (-NH2) and ammonium (-NH3+) groups in glycine effectively passivate Sn4+ defects at the buried interface of Sn-Pb perovskite films, even under thermal stress. Consequently, the synergistic buried interface regulation of Co-SAM leads to a power conversion efficiency (PCE) of 23.46%, which outperforms devices modified with 2PACz or glycine alone. The Co-SAM-modified Sn-Pb PSC demonstrates enhanced thermal stability, maintaining 88% of its initial PCE under 65 °C thermal stress for 590 h.

New Insights in the Computational pKb Determination of Primary Amines and Anilines

Extensive research has already provided reliable methods for the in silico prediction of pKa, while a trustworthy strategy for pKb determination is still being sought. Indeed, the approaches previously exploited for computing pKa have shown their weakness in predicting pKb. In the light of the exceptional reliability demonstrated in the pKa calculation of a wide panel of organic acids, in this work, we exploited our "easy to use methodology", based on the direct approach, to predict the pKb of primary amines. Herein, CAM-B3LYP was compared to WB97XD and B3PW91, exploring the solvation model based on density (SMD) and the polarizable continuum model (PCM), in the presence of two explicit water molecules. Noteworthy, CAM-B3LYP and WB97XD returned completely different solvent accessible surfaces (SAS) and electron potential maps (EPM) for the bases and the conjugated acids, independently from the nature of the substituents. Once again, CAM-B3LYP/SMD/2H2O method confirmed its remarkable reliability, leading to a minimum average error (MAE) lower than 0.3. This outstanding result strengthens the trustworthiness of our method, already successfully applied to predict the pKa of different substituted phenols and carboxylic acids. Thus, our "easy-to-use" process can predict also the pKb of primary ammines and anilines, always ensuring consistent outputs.

A comprehensive electron wavefunction analysis toolbox for chemists, Multiwfn

Analysis of electron wavefunction is a key component of quantum chemistry investigations and is indispensable for the practical research of many chemical problems. After more than ten years of active development, the wavefunction analysis program Multiwfn has accumulated very rich functions, and its application scope has covered numerous aspects of theoretical chemical research, including charge distribution, chemical bond, electron localization and delocalization, aromaticity, intramolecular and intermolecular interactions, electronic excitation, and response property. This article systematically introduces the features and functions of the latest version of Multiwfn and provides many representative examples. Through this article, readers will be able to fully understand the characteristics and recognize the unique value of Multiwfn. The source code and precompiled executable files of Multiwfn, as well as the manual containing a detailed introduction to theoretical backgrounds and very rich tutorials, can all be downloaded for free from the Multiwfn website (http://sobereva.com/multiwfn).

High-Throughput Screening and Prediction of Nucleophilicity of Amines Using Machine Learning and DFT Calculations

Nucleophilic index (NNu) as a significant parameter plays a crucial role in screening of amine catalysts. Indeed, the quantity and variety of amines are extensive. However, only limited amines exhibit an NNu value exceeding 4.0 eV, rendering them potential nucleophiles in chemical reactions. To address this issue, we proposed a computational method to quickly identify amines with high NNu values by using Machine Learning (ML) and high-throughput Density Functional Theory (DFT) calculations. Our approach commenced by training ML models and the exploration of Molecular Fingerprint methods as well as the development of quantitative structure-activity relationship (QSAR) models for the well-known amines based on NNu values derived from DFT calculations. Utilizing explainable Shapley Additive Explanation plots, we were able to determine the five critical substructures that significantly impact the NNu values of amine. The aforementioned conclusion can be applied to produce and cultivate 4920 novel hypothetical amines with high NNu values. The QSAR models were employed to predict the NNu values of 259 well-known and 4920 hypothetical amines, resulting in the identification of five novel hypothetical amines with exceptional NNu values (>4.55 eV). The enhanced NNu values of these novel amines were validated by DFT calculations. One novel hypothetical amine, H1, exhibits an unprecedentedly high NNu value of 5.36 eV, surpassing the maximum value (5.35 eV) observed in well-established amines. Our research strategy efficiently accelerates the discovery of the high nucleophilicity of amines using ML predictions, as well as the DFT calculations.

Reliable and accurate prediction of basic pK[Formula: see text] values in nitrogen compounds: the pK[Formula: see text] shift in supramolecular systems as a case study

This article presents a quantitative structure-activity relationship (QSAR) approach for predicting the acid dissociation constant (pK[Formula: see text]) of nitrogenous compounds, including those within supramolecular complexes based on cucurbiturils. The model combines low-cost quantum mechanical calculations with QSAR methodology and linear regressions to achieve accurate predictions for a broad range of nitrogen-containing compounds. The model was developed using a diverse dataset of 130 nitrogenous compounds and exhibits excellent predictive performance, with a high coefficient of determination (R[Formula: see text]) of 0.9905, low standard error (s) of 0.3066, and high Fisher statistic (F) of 2142. The model outperforms existing methods, such as Chemaxon software and previous studies, in terms of accuracy and its ability to handle heterogeneous datasets. External validation on pharmaceutical ingredients, dyes, and supramolecular complexes based on cucurbiturils confirms the reliability of the model. To enhance usability, a script-like tool has been developed, providing a streamlined process for users to access the model. This study represents a significant advancement in pK[Formula: see text] prediction, offering valuable insights for drug design and supramolecular system optimization.

Seeking the most stable isomer of azahomocubanes

This study examines the stability and protonation properties of four potential azahomocubanes. Through high-level ab initio computations, we find that 9-azahomocubane is the most stable isomer, closely followed by 5-azahomocubane, 1-azahomocubane, and 2-azahomocubane. However, understanding the stability of the systems with a nitrogen atom incorporated into a highly constrained polycyclic environment extends beyond mere bond angles or hybridization considerations. Strain energy analysis reveals that azahomocubanes experience less strain compared to their carbon congeners. An exploration of multiple solvents shows that their impact on relative energies and geometries is negligible. On the other hand, among the four isomers, 2-azahomocubane exhibits the highest tendency for protonation. Basicity, as assessed through the minimum electrostatic potential, correlates well with protonation affinities.

Reactivity of the Iboga Skeleton: Oxidation Study of Ibogaine and Voacangine

The iboga alkaloids scaffold shows great potential as a pharmacophore in drug candidates for the treatment of neuropsychiatric disorders. Thus, the study of the reactivity of this type of motif is particularly useful for the generation of new analogs suitable for medicinal chemistry goals. In this article, we analyzed the oxidation pattern of ibogaine and voacangine using dioxygen, peroxo compounds, and iodine as oxidizing agents. Special focus was placed on the study of the regio- and stereochemistry of the oxidation processes according to the oxidative agent and starting material. We found that the C16-carboxymethyl ester present in voacangine stabilizes the whole molecule toward oxidation in comparison to ibogaine, especially in the indole ring, where 7-hydroxy- or 7-peroxy-indolenines can be obtained as oxidation products. Nevertheless, the ester moiety enhances the reactivity of the isoquinuclidinic nitrogen to afford C3-oxidized products through a regioselective iminium formation. This differential reactivity between ibogaine and voacangine was rationalized using computational DFT calculations. In addition, using qualitative and quantitative NMR experiments combined with theoretical calculations, the absolute stereochemistry at C7 in the 7-hydroxyindolenine of voacangine was revised to be S, which corrects previous reports proposing an R configuration.

A density fitting scheme for the fast evaluation of molecular electrostatic potential

Molecular electrostatic potential (MEP) is a significant and crucial physical quantity that can be applied to a large number of scenarios, such as the prediction of nucleophilic or electrophilic attacks, fitting atomic charges, σ-hole, and so forth. The computational cost for the MEP has an O(N² ) scaling with the increase of atoms, which is intractable and laborious for macromolecules. Herein, a density fitting molecular electrostatic potential (DF-MEP) is used to reduce the computational costs for the macromolecular MEP. It is found that the accuracy of DF-MEP is almost identical to the conventional molecular electrostatic potential (Conv-MEP), while the computational costs can be reduced to an O(N) scaling, for example, the computational time of 699,200 grids for the Trp-cage molecule (304 atoms) only takes 16.6 s at the B3LYP-D3(BJ)/def2-SVP level of theory with 16 CPU cores compared with 3060.2 s for the Conv-MEP method.

Competing on the same stage: Ru-based catalysts modified by basic ligands and organic chlorine salts for acetylene hydrochlorination

To provide reference for the search of efficient ligands for acetylene hydrochlorination, various basic ligands with different alkaline gradients have been employed to modify Ru-based catalysts, and a rule is...

N-Triflylphosphoramides: highly acidic catalysts for asymmetric transformations

N-Triflylphosphoramides (NTPA), have become increasingly popular catalysts in the development of enantioselective transformations as they are stronger Brønsted acids than the corresponding phosphoric acids (PA). Their highly acidic, asymmetric active site can activate difficult, unreactive substrates. In this review, we present an account of asymmetric transformations using this type of catalyst that have been reported in the past ten years and we classify these reactions using the enantio-determining step as the key criterion. This compendium of NTPA-catalysed reactions is organised into the following categories: (1) cycloadditions, (2) electrocyclisations, polyene and related cyclisations, (3) addition reactions to imines, (4) electrophilic aromatic substitutions, (5) addition reactions to carbocations, (6) aldol and related reactions, (7) addition reactions to double bonds, and (8) rearrangements and desymmetrisations. We highlight the use of NTPA in total synthesis and suggest mnemonics which account for their enantioselectivity.

Recuperative Amino Acids Separation through Cellulose Derivative Membranes with Microporous Polypropylene Fiber Matrix

The separation, concentration and transport of the amino acids through membranes have been continuously developed due to the multitude of interest amino acids of interest and the sources from which they must be recovered. At the same time, the types of membranes used in the sepa-ration of the amino acids are the most diverse: liquids, ion exchangers, inorganic, polymeric or composites. This paper addresses the recuperative separation of three amino acids (alanine, phe-nylalanine, and methionine) using membranes from cellulosic derivatives in polypropylene ma-trix. The microfiltration membranes (polypropylene hollow fibers) were impregnated with solu-tions of some cellulosic derivatives: cellulose acetate, 2-hydroxyethyl-cellulose, methyl 2-hydroxyethyl-celluloseand sodium carboxymethyl-cellulose. The obtained membranes were characterized in terms of the separation performance of the amino acids considered (retention, flux, and selectivity) and from a morphological and structural point of view: scanning electron microscopy (SEM), high resolution SEM (HR-SEM), Fourier transform infrared spectroscopy (FT-IR), energy dispersive spectroscopy (EDS) and thermal gravimetric analyzer (TGA). The re-sults obtained show that phenylalanine has the highest fluxes through all four types of mem-branes, followed by methionine and alanine. Of the four kinds of membrane, the most suitable for recuperative separation of the considered amino acids are those based on cellulose acetate and methyl 2-hydroxyethyl-cellulose.

Transport of Amino Acids in Soy Sauce Desalination Process by Electrodialysis

Soy sauce is a common condiment that has a unique flavor, one that is derived from its rich amino acids and salts. It is known that excessive intake of high-sodium food will affect human health, causing a series of diseases such as hypertension and kidney disease. Therefore, removing sodium from the soy sauce and retaining the amino acids is desirable. In this study, electrodialysis (ED) was employed for the desalination of soy sauce using commercial ion exchange membranes (IEMs). The influence of the current density and initial pH on the desalination degree of the soy sauce was explored. Results showed that the optimal desalination condition for ED was reached at a current density of 5 mA/cm² and pH of 5, with the desalination degree of 64% and the amino acid loss rate of 29.8%. Moreover, it was found that the loss rate of amino acids was related to the initial concentration and molecular structure. In addition, the amino acid adsorption by IEMs was explored. Results implied that the molecular weight and structure affect amino acid adsorption. This study illustrated that the ED process can successfully reduce the salt content of the soy sauce and retain most of the amino acids without compromising the original flavor.

Partitioning Pattern of Natural Products Based on Molecular Properties Descriptors Representing Drug-Likeness

A cheminformatics procedure for a partitioning model based on 135 natural compounds including Flavonoids, Saponins, Alkaloids, Terpenes and Triterpenes with drug-like features based on a descriptors pool was developed. The knowledge about the applicability of natural products as a unique source for the development of new candidates towards deadly infectious disease is a contemporary challenge for drug discovery. We propose a partitioning scheme for unveiling drug-likeness candidates with properties that are important for a prompt and efficient drug discovery process. In the present study, the vantage point is about the matching of descriptors to build the partitioning model applied to natural compounds with diversity in structures and complexity of action towards the severe diseases, as the actual SARS-CoV-2 virus. In the times of the de novo design techniques, such tools based on a chemometric and symmetrical effect by the implied descriptors represent another noticeable sign for the power and level of the descriptors applicability in drug discovery in establishing activity and target prediction pipeline for unknown drugs properties.

Tuning the Reactivity and Bonding Properties of Metal Square-Planar Complexes by the Substitution(s) on the Trans-Coordinated Pyridine Ring

The kinetics of the hydration reaction on trans-[Pt(NH₃)₂(pyrX)Cl]⁺ (pyr = pyridine) complexes (X = OH^-, Cl^-, F^-, Br^-, NO₂ ^-, NH₂, SH^-, CH₃, C≡CH, and DMA) was studied by density functional theory calculations in the gas phase and in water solution described by the implicit polarizable continuum model method. All possible positions ortho, meta, and para of the substituent X in the pyridine ring were considered. The substitution of the pyr ligand by electron-donating X's led to the strengthening of the Pt-N1(pyrX) (Pt-N_pyrX) bond and the weakening of the trans Pt-Cl or Pt-O_w bonds. The electron-withdrawing X's have exactly the opposite effect. The strengths of these bonds can be predicted from the basicity of sigma electrons on the N_pyrX atom determined on the isolated pyrX ligand. As the pyrX ring was oriented perpendicularly with respect to the plane of the complex, the nature of the X···Cl electrostatic interaction was the decisive factor for the transition-state (TS) stabilization which resulted in the highest selectivity of ortho-substituted systems with respect to the reaction rate. Because of a smaller size of X's, the steric effects influenced less importantly the values of activation Gibbs energies ΔG ^⧧ but caused geometry changes such as the elongation of the Pt-N_pyrX bonds. Substitution in the meta position led to the highest ΔG ^⧧ values for most of the X's. The changes of ΔG ^⧧ because of electronic effects were the same in the gas phase and the water solvent. However, as the water solvent dampened electrostatic interactions, 2200 and 150 times differences in the reaction rate were observed between the most and the least reactive mono-substituted complexes in the gas phase and the water solvent, respectively. An additional NO₂ substitution of the pyrNO₂ ligand further decelerated the rate of the hydration reaction, but on the other hand, the poly-NH₂ complexes were no more reactive than the fastest o-NH₂ system. In the gas phase, the poly-X complexes showed the additivity of the substituent effects with respect to the Pt-ligand bond strengths and the ligand charges.