Molecules

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19 pages, 6021 KiB

Open AccessArticle

Electron Density and Molecular Orbital Analyses of the Nature of Bonding in the η³-CCH Agostic Rhodium Complexes Preceding the C–C and C–H Bond Cleavages

by Irena Efremenko

Molecules 2024, 29(20), 4788; https://doi.org/10.3390/molecules29204788 - 10 Oct 2024

Viewed by 781

Abstract

In our recent work, we revisited C–H and C–C bond activation in rhodium (I) complexes of pincer ligands PCP, PCN, PCO, POCOP, and SCS. Our findings indicated that an η³-C_sp2C_sp3H agostic intermediate acts as a common precursor [...] Read more.

In our recent work, we revisited C–H and C–C bond activation in rhodium (I) complexes of pincer ligands PCP, PCN, PCO, POCOP, and SCS. Our findings indicated that an η³-C_sp2C_sp3H agostic intermediate acts as a common precursor to both C–C and C–H bond activation in these systems. We explore the electronic structure and bonding nature of these precleavage complexes using electron density and molecular orbital analyses. Using NBO, IBO, and ESI-3D methods, the bonding in the η³-CCH agostic moiety is depicted by two three-center agostic bonds: Rh–C_sp2–C_sp3 and Rh–C_sp3–H, with all three atoms datively bound to Rh(I). IBO analysis specifically highlights the involvement of three orbitals (CC→Rh and CH→Rh σ donation, plus Rh→CCH π backdonation) in both C–C and C–H bond cleavages. NCIPLOT and QTAIM analyses highlight anagostic (Rh–H) or β-agostic (Rh–C_sp2–H) interactions and the absence of Rh–C_sp³ interactions. QTAIM molecular graphs suggest bond path instability under dynamic conditions due to the nearness of line and ring critical points. Several low-frequency and low-force vibrational modes interconvert various bonding patterns, reinforcing the dynamic η³-CCH agostic nature. The kinetic preference for C–H bond breaking is attributed to the smaller reduced mass of C–H vibrations compared to C–C vibrations. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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17 pages, 4784 KiB

Open AccessArticle

Synthesis of an Ethylenediaminetetraacetic Acid-like Ligand Based on Sucrose Scaffold and Complexation and Proton Relaxivity Studies of Its Gadolinium(III) Complex in Solution

by Ping Zhang, Cécile Barbot, Ramakrishna Gandikota, Cenxiao Li, Laura Gouriou, Géraldine Gouhier and Chang-Chun Ling

Molecules 2024, 29(19), 4688; https://doi.org/10.3390/molecules29194688 - 3 Oct 2024

Viewed by 595

Abstract

Sucrose constitutes a non-toxic, biodegradable, low-cost and readily available natural product. To expand its utility, we developed total synthesis for a ligand based on a sucrose scaffold for potential use as a metal chelation agent. The designed target (compound 2) has a [...] Read more.

Sucrose constitutes a non-toxic, biodegradable, low-cost and readily available natural product. To expand its utility, we developed total synthesis for a ligand based on a sucrose scaffold for potential use as a metal chelation agent. The designed target (compound 2) has a metal-chelating functionality at both the C-6 and C-6’ positions, which can provide a first coordination sphere of eight valencies. The designed total synthesis was highly efficient. To demonstrate the utility of the ligand, we studied its complexation with Gd(III). Using potentiometric titration and high-resolution mass spectrometry, we confirmed the formation of a 1:1 complex with Gd(III), which has a respectable formation constant of ~10^13.4. Further NMR relaxivity studies show that the Gd(III) complex has a relaxivity (r1) of 7.6958 mmol⁻¹ s⁻¹. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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19 pages, 2197 KiB

Open AccessArticle

Antimicrobial Activity of Anionic Bis(N-Heterocyclic Carbene) Silver Complexes

by Carlos J. Carrasco, Francisco Montilla, Eduardo Villalobo, Manuel Angulo, Eleuterio Álvarez and Agustín Galindo

Molecules 2024, 29(19), 4608; https://doi.org/10.3390/molecules29194608 - 27 Sep 2024

Viewed by 587

Abstract

The antimicrobial properties of a series of anionic bis(carbene) silver complexes Na₃[Ag(NHC^R)₂] were investigated (2a–2g and 2c′, where NHC^R is a 2,2′-(imidazol-2-ylidene)dicarboxylate-type N-heterocyclic carbene). The complexes were synthesized by the interaction [...] Read more.

The antimicrobial properties of a series of anionic bis(carbene) silver complexes Na₃[Ag(NHC^R)₂] were investigated (2a–2g and 2c′, where NHC^R is a 2,2′-(imidazol-2-ylidene)dicarboxylate-type N-heterocyclic carbene). The complexes were synthesized by the interaction of imidazolium dicarboxylate compounds with silver oxide in the presence of aqueous sodium hydroxide. Complexes 2f,g were characterized analytically and spectroscopically, and the ligand precursor 1f and complexes 2c and 2g were structurally identified by X-ray diffraction methods. The anions of 2c and 2g, [Ag(NHC^R)₂]³⁻, showed a typical linear disposition of C_carbene-Ag-C_carbene atoms and an uncommonly eclipsed conformation of carbene ligands. The antimicrobial properties of complexes 2a–g, which contains chiral (2b–2e and 2c′) and non-chiral derivatives (2a,f,g), were evaluated against Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa, and a Gram-positive bacterium, Staphylococcus aureus. From the observed values of the minimal inhibitory concentration and minimal bactericidal concentration, complexes 2a and 2b showed the best antimicrobial activity against all strains. An interesting chirality–antimicrobial relationship was found, and eutomer 2c′ showed better activity than its enantiomer 2c against the three bacteria. Furthermore, these complexes were investigated experimentally and theoretically by ¹⁰⁹Ag nuclear magnetic resonance, and the electronic and steric characteristics of the dianionic carbene ligands were also examined. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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11 pages, 4932 KiB

Open AccessArticle

Engineering Novel Amphiphilic Platinum(IV) Complexes to Co-Deliver Cisplatin and Doxorubicin

by Wjdan Jogadi, Man B. Kshetri, Suha Alqarni, Arpit Sharma, May Cheline, Md Al Amin, Cynthia Sheets, Angele Nsoure-Engohang and Yao-Rong Zheng

Molecules 2024, 29(17), 4095; https://doi.org/10.3390/molecules29174095 - 29 Aug 2024

Viewed by 693

Abstract

In this study, we report a novel platinum–doxorubicin conjugate that demonstrates superior therapeutic indices to cisplatin, doxorubicin, or their combination, which are commonly used in cancer treatment. This new molecular structure (1) was formed by conjugating an amphiphilic Pt(IV) prodrug of [...] Read more.

In this study, we report a novel platinum–doxorubicin conjugate that demonstrates superior therapeutic indices to cisplatin, doxorubicin, or their combination, which are commonly used in cancer treatment. This new molecular structure (1) was formed by conjugating an amphiphilic Pt(IV) prodrug of cisplatin with doxorubicin. Due to its amphiphilic nature, the Pt(IV)–doxorubicin conjugate effectively penetrates cell membranes, delivering both cisplatin and doxorubicin payloads intracellularly. The intracellular accumulation of these payloads was assessed using graphite furnace atomic absorption spectrometry and fluorescence imaging. Since the therapeutic effects of cisplatin and doxorubicin stem from their ability to target nuclear DNA, we hypothesized that the amphiphilic Pt(IV)–doxorubicin conjugate (1) would effectively induce nuclear DNA damage toward killing cancer cells. To test this hypothesis, we used flow the cytometric analysis of phosphorylated H2AX (γH2AX), a biomarker of nuclear DNA damage. The Pt(IV)–doxorubicin conjugate (1) markedly induced γH2AX in treated MDA-MB-231 breast cancer cells, showing higher levels than cells treated with either cisplatin or doxorubicin alone. Furthermore, MTT cell viability assays revealed that the enhanced DNA-damaging capability of complex 1 resulted in superior cytotoxicity and selectivity against human cancer cells compared to cisplatin, doxorubicin, or their combination. Overall, the development of this amphiphilic Pt(IV)–doxorubicin conjugate represents a new form of combination therapy with improved therapeutic efficacy. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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11 pages, 4222 KiB

Open AccessArticle

Design of pH/Redox Co-Triggered Degradable Diselenide-Containing Polyprodrug via a Facile One-Pot Two-Step Approach for Tumor-Specific Chemotherapy

by Yanru Hu and Peng Liu

Molecules 2024, 29(16), 3837; https://doi.org/10.3390/molecules29163837 - 13 Aug 2024

Viewed by 814

Abstract

The diselenide bond has attracted intense interest for drug delivery systems (DDSs) for tumor chemotherapy, owing to it possessing higher redox sensitivity than the disulfide one. Various redox-responsive diselenide-containing carriers have been developed for chemotherapeutics delivery. However, the premature drug leakage from these [...] Read more.

The diselenide bond has attracted intense interest for drug delivery systems (DDSs) for tumor chemotherapy, owing to it possessing higher redox sensitivity than the disulfide one. Various redox-responsive diselenide-containing carriers have been developed for chemotherapeutics delivery. However, the premature drug leakage from these DDSs was significant enough to cause toxic side effects on normal cells. Here, a pH/redox co-triggered degradable polyprodrug was designed as a drug self-delivery system (DSDS) by incorporating drug molecules as structural units in the polymer main chains, using a facile one-pot two-step approach. The proposed PDOX could only degrade and release drugs by breaking both the neighboring acid-labile acylhydrazone and the redox-cleavable diselenide conjugations in the drug’s structural units, triggered by the higher acidity and glutathione (GSH) or reactive oxygen species (ROS) levels in the tumor cells. Therefore, a slow solubility-controlled drug release was achieved for tumor-specific chemotherapy, indicating promising potential as a safe and efficient long-acting DSDS for future tumor treatment. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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33 pages, 6911 KiB

Open AccessArticle

Designing Accurate Moment Tensor Potentials for Phonon-Related Properties of Crystalline Polymers

by Lukas Reicht, Lukas Legenstein, Sandro Wieser and Egbert Zojer

Molecules 2024, 29(16), 3724; https://doi.org/10.3390/molecules29163724 - 6 Aug 2024

Viewed by 1120

Abstract

The phonon-related properties of crystalline polymers are highly relevant for various applications. Their simulation is, however, particularly challenging, as the systems that need to be modeled are often too extended to be treated by ab initio methods, while classical force fields are too [...] Read more.

The phonon-related properties of crystalline polymers are highly relevant for various applications. Their simulation is, however, particularly challenging, as the systems that need to be modeled are often too extended to be treated by ab initio methods, while classical force fields are too inaccurate. Machine-learned potentials parametrized against material-specific ab initio data hold the promise of being extremely accurate and also highly efficient. Still, for their successful application, protocols for their parametrization need to be established to ensure an optimal performance, and the resulting potentials need to be thoroughly benchmarked. These tasks are tackled in the current manuscript, where we devise a protocol for parametrizing moment tensor potentials (MTPs) to describe the structural properties, phonon band structures, elastic constants, and forces in molecular dynamics simulations for three prototypical crystalline polymers: polyethylene (PE), polythiophene (PT), and poly-3-hexylthiophene (P3HT). For PE, the thermal conductivity and thermal expansion are also simulated and compared to experiments. A central element of the approach is to choose training data in view of the considered use case of the MTPs. This not only yields a massive speedup for complex calculations while essentially maintaining DFT accuracy, but also enables the reliable simulation of properties that, so far, have been entirely out of reach. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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18 pages, 4178 KiB

Open AccessArticle

Atomistic Origins of Resurrection of Aged Acetylcholinesterase by Quinone Methide Precursors

by Leonardo V. F. Ferreira, Taináh M. R. Santos, Camila A. Tavares, Hassan Rasouli and Teodorico C. Ramalho

Molecules 2024, 29(15), 3684; https://doi.org/10.3390/molecules29153684 - 3 Aug 2024

Viewed by 910

Abstract

Nerve agents are organophosphates (OPs) that act as potent inhibitors of acetylcholinesterase (AChE), the enzyme responsible for the hydrolysis of acetylcholine. After inhibition, a dealkylation reaction of the phosphorylated serine, known as the aging of AChE, can occur. When aged, reactivators of OP-inhibited [...] Read more.

Nerve agents are organophosphates (OPs) that act as potent inhibitors of acetylcholinesterase (AChE), the enzyme responsible for the hydrolysis of acetylcholine. After inhibition, a dealkylation reaction of the phosphorylated serine, known as the aging of AChE, can occur. When aged, reactivators of OP-inhibited AChE are no longer effective. Therefore, the realkylation of aged AChE may offer a pathway to reverse AChE aging. In this study, molecular modeling was conducted to propose new ligands as realkylators of aged AChE. We applied a methodology involving docking and quantum mechanics/molecular mechanics (QM/MM) calculations to evaluate the resurrection kinetic constants and ligand interactions with OP-aged AChE, comparing them to data found in the literature. The results obtained confirm that this method is suitable for predicting kinetic and thermodynamic parameters of ligands, which can be useful in the design and selection of new and more effective ligands for AChE realkylation. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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14 pages, 3672 KiB

Open AccessArticle

Synthesis and Characterization of Symmetrical N-Heterocyclic Carbene Copper(II) Complexes—An Investigation of the Influence of Pyridinyl Substituents

by Bhupendra Adhikari, Selvam Raju, Raymond Femi Awoyemi, Bruno Donnadieu, David O. Wipf, Sean L. Stokes and Joseph P. Emerson

Molecules 2024, 29(15), 3542; https://doi.org/10.3390/molecules29153542 - 27 Jul 2024

Viewed by 962

Abstract

Three new tridentate copper(II) N-heterocyclic carbene (NHC) complexes have been obtained and characterized with symmetrical C-4 substitutions on their pendent pyridine rings. Substitutions including methyl (Me), methoxy (OMe), and chloro (Cl) groups, which extend the library pincer Cu-NHC complexes under investigation, modify [...] Read more.

Three new tridentate copper(II) N-heterocyclic carbene (NHC) complexes have been obtained and characterized with symmetrical C-4 substitutions on their pendent pyridine rings. Substitutions including methyl (Me), methoxy (OMe), and chloro (Cl) groups, which extend the library pincer Cu-NHC complexes under investigation, modify the impact of pyridinyl basicity on NCN pincer complexes. Both ligand precursors and copper(II) complexes are characterized using a range of techniques, including nuclear magnetic resonance (NMR) spectroscopy for ¹H, ¹³C, ³¹P, and ¹⁹F nuclei, electrospray ionization mass spectrometry (ESI-MS), X-ray crystallography, cyclic voltammetry, and UV-Vis spectroscopy. The pyridine substitutions lead to minimal changes to bond lengths and angles in the X-ray crystal structures of these related complexes; there is a pronounced impact on the electrochemical behavior of both the ligand precursors and copper complexes in the solution. The substitution in the pyridinyl units of these complexes show an impact on the catalytic reactivity of these complexes as applied to a model C–N bond-forming reaction (CEL cross-coupling) under well-established conditions; however, this observation does not correlate to the expected change in basicity in these ligands. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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15 pages, 3578 KiB

Open AccessArticle

Combined Theoretical and Experimental Investigations: Design, Synthesis, Characterization, and In Vitro Cytotoxic Activity Assessment of a Complex of a Novel Ureacellobiose Drug Carrier with the Anticancer Drug Carmustine

by Marta Hoelm, Stanisław Porwański, Paweł Jóźwiak and Anna Krześlak

Molecules 2024, 29(14), 3359; https://doi.org/10.3390/molecules29143359 - 17 Jul 2024

Viewed by 995

Abstract

Drug delivery systems (DDSs) are used to transport drugs which are characterized by some pharmaceutical problems to the specific target site, enhancing therapeutic efficacy and reducing off-target accumulation in the body. In this work, one of the recently synthesized molecules, 1,10-N, [...] Read more.

Drug delivery systems (DDSs) are used to transport drugs which are characterized by some pharmaceutical problems to the specific target site, enhancing therapeutic efficacy and reducing off-target accumulation in the body. In this work, one of the recently synthesized molecules, 1,10-N,N’-bis-(β-ᴅ-ureidocellobiosyl)-4,7,13,16-tetraoxa-1,10-diazacyclooctadecane (TN), was tested as a potential drug carrier towards the anticancer drug carmustine. For this purpose, different techniques were used, from synthesis and calculations to cytotoxicity assessment. Our results showed that TN is characterized by a very compact geometry, which significantly impacts its complexation properties. Although it forms a very stable complex with carmustine, it adopts a non-inclusion geometry, as verified by both experimental and theoretical NMR analyses. The cytotoxicity study performed for all analyzed molecules (TN; carmustine; TN:carmustine complex) towards normal and cancer (breast and colon) cells revealed that TN is not toxic and that the formation of complexes with carmustine reduces the toxicity of carmustine to normal cells. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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20 pages, 12152 KiB

Open AccessArticle

Theoretical Analysis of Coordination Geometries in Transition Metal–Histidine Complexes Using Quantum Chemical Calculations

by Dapeng Zhang and Naoki Kishimoto

Molecules 2024, 29(13), 3003; https://doi.org/10.3390/molecules29133003 - 25 Jun 2024

Cited by 1 | Viewed by 1083

Abstract

A theoretical investigation utilizing density functional theory (DFT) calculations was conducted to explore the coordination complexes formed between histidine (His) ligands and various divalent transition metal ions (Mn²⁺, Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺, and [...] Read more.

A theoretical investigation utilizing density functional theory (DFT) calculations was conducted to explore the coordination complexes formed between histidine (His) ligands and various divalent transition metal ions (Mn²⁺, Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺). Conformational exploration of the His ligand was initially performed to assess its stability upon coordination. Both 1:1 and 1:2 of metal-to-ligand complexes were scrutinized to elucidate their structural features and the relative stability of the complexes. This study examined the ability of His to act as a bidentate or tridentate coordinating ligand, along with the differences in coordination geometry when solvent effects were incorporated. The reduced density gradient (RDG) analysis and local electron attachment energy (LEAE) analysis were employed to elucidate the interaction planes and the nucleophilic and electrophilic properties. The electronic properties were analyzed through electrostatic potential (ESP) maps and natural population analysis (NPA) of atomic charge distributions. This computational study provides valuable insights into the diverse coordination modes of His and its interactions with divalent transition metal ions, contributing to a better understanding of the role of this amino acid ligand in the formation of transition metal complexes. The findings can aid in the design and construction of self-assembled structures involving His-metal coordination. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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10 pages, 1209 KiB

Open AccessCommunication

Modeling Peptide–Protein Interactions by a Logo-Based Method: Application in Peptide–HLA Binding Predictions

by Irini Doytchinova, Mariyana Atanasova, Antonio Fernandez, F. Javier Moreno, Frits Koning and Ivan Dimitrov

Molecules 2024, 29(2), 284; https://doi.org/10.3390/molecules29020284 - 5 Jan 2024

Cited by 1 | Viewed by 1361

Abstract

Peptide–protein interactions form a cornerstone in molecular biology, governing cellular signaling, structure, and enzymatic activities in living organisms. Improving computational models and experimental techniques to describe and predict these interactions remains an ongoing area of research. Here, we present a computational method for [...] Read more.

Peptide–protein interactions form a cornerstone in molecular biology, governing cellular signaling, structure, and enzymatic activities in living organisms. Improving computational models and experimental techniques to describe and predict these interactions remains an ongoing area of research. Here, we present a computational method for peptide–protein interactions’ description and prediction based on leveraged amino acid frequencies within specific binding cores. Utilizing normalized frequencies, we construct quantitative matrices (QMs), termed ‘logo models’ derived from sequence logos. The method was developed to predict peptide binding to HLA-DQ2.5 and HLA-DQ8.1 proteins associated with susceptibility to celiac disease. The models were validated by more than 17,000 peptides demonstrating their efficacy in discriminating between binding and non-binding peptides. The logo method could be applied to diverse peptide–protein interactions, offering a versatile tool for predictive analysis in molecular binding studies. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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11 pages, 1796 KiB

Open AccessArticle

Synthesis, Structure, and Characterizations of a Volatile/Soluble Heterometallic Hexanuclear Precursor [NaMn₂(thd)₄(OAc)]₂

by Yuxuan Zhang, Zheng Wei and Evgeny V. Dikarev

Molecules 2023, 28(23), 7795; https://doi.org/10.3390/molecules28237795 - 27 Nov 2023

Cited by 1 | Viewed by 1046

Abstract

The paper describes a heterobimetallic mixed-ligand hexanuclear precursor [NaMn₂(thd)₄(OAc)]₂ (1) (thd = 2,2,6,6-tetramethyl-3,5-heptadionate; OAc = acetate) that was designed based on its lithium homoleptic analogue, [LiMn₂(thd)₅], by replacing one of [...] Read more.

The paper describes a heterobimetallic mixed-ligand hexanuclear precursor [NaMn₂(thd)₄(OAc)]₂ (1) (thd = 2,2,6,6-tetramethyl-3,5-heptadionate; OAc = acetate) that was designed based on its lithium homoleptic analogue, [LiMn₂(thd)₅], by replacing one of the thd ligands with an acetate group in order to accommodate 5-coordinated sodium instead of tetrahedral lithium ion. The complex, which is highly volatile and soluble in a variety of common solvents, has been synthesized by both the solid-state and solution methods. The unique “dimer-of-trimers” heterometallic structure consists of two trinuclear [NaMn^II₂(thd)₄]⁺ units firmly bridged by two acetate ligands. X-ray diffraction techniques, DART mass spectrometry, ICP-OES analysis, and IR spectroscopy have been employed to confirm the structure and composition of the hexanuclear complex. Similar to the Li counterpart forming LiMn₂O₄ spinel material upon thermal decomposition, the title Na:Mn = 1:2 compound was utilized as the first single-source precursor for the low-temperature preparation of Na₄Mn₉O₁₈ tunnel oxide. Importantly, four Mn sites in the hexanuclear molecule can be potentially partially substituted by other transition metals, leading to heterotri- and tetrametallic precursors for the advanced quaternary and quinary Na-ion oxide cathode materials. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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19 pages, 3156 KiB

Open AccessArticle

NMR “Finger Prints” of N-Heterocyclic Carbenes, DFT Analysis: Scopes and Limitations

by Svetlana A. Kondrashova and Shamil K. Latypov

Molecules 2023, 28(23), 7729; https://doi.org/10.3390/molecules28237729 - 23 Nov 2023

Cited by 1 | Viewed by 1022

Abstract

The scopes and limitations of theoretical methods for estimating various NMR metrics of NHCs are considered on a wide range of model NHCs and their derivatives, using a number of computational approximations. On the whole, the most reliable, from the point of view [...] Read more.

The scopes and limitations of theoretical methods for estimating various NMR metrics of NHCs are considered on a wide range of model NHCs and their derivatives, using a number of computational approximations. On the whole, the most reliable, from the point of view of predictability and insusceptibility to additional effects, are ³¹P/¹³C NMR shifts of NHC–phosphinidene adducts and ¹³C CSs of carbenes themselves. The method based on the analysis of ⁷⁷Se CS NHC–selenoureas has some limitations since the observed NMR parameters can also be modulated by exchange effects due to their formation with non-classical hydrogen bonds. As for HEP, since the delicate balance of electron distribution between Pd and two carbon centers can nonlinearly affect relativistic spin–orbit effects, the accuracy of the estimation of this metric may still be limited. ¹³C CSs of NHC–azolium salts do not seem to be reliable, since the observed values are strongly influenced by the effects of the exchange between different forms with counterions, which are difficult to estimate correctly. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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8 pages, 3369 KiB

Open AccessCommunication

Directional Crystallization of Conjugated Molecules during Coating Processes

by Detlef-M. Smilgies and Ruipeng Li

Molecules 2023, 28(14), 5371; https://doi.org/10.3390/molecules28145371 - 13 Jul 2023

Viewed by 924

Abstract

The coating of organic molecules from the solution phase can result in directional crystal growth under certain conditions, even on a smooth isotropic surface and without the need of any kind of graphoexpitaxial preparation of the substrate. Based on reviewing the results from [...] Read more.

The coating of organic molecules from the solution phase can result in directional crystal growth under certain conditions, even on a smooth isotropic surface and without the need of any kind of graphoexpitaxial preparation of the substrate. Based on reviewing the results from a variety of coating techniques and coating parameters, we identified that it is crucial for the coating speed to match the growth speed of the fastest growing crystal plane to achieve a high degree of directional crystallization. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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17 pages, 2505 KiB

Open AccessArticle

Silver Ion High-Performance Liquid Chromatography—Atmospheric Pressure Chemical Ionization Mass Spectrometry: A Tool for Analyzing Cuticular Hydrocarbons

by Vladimír Vrkoslav, Petra Horká, Jindřich Jindřich, Miloš Buděšínský and Josef Cvačka

Molecules 2023, 28(9), 3794; https://doi.org/10.3390/molecules28093794 - 28 Apr 2023

Cited by 1 | Viewed by 2007

Abstract

Aliphatic hydrocarbons (HCs) are usually analyzed by gas chromatography (GC) or matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. However, analyzing long-chain HCs by GC is difficult because of their low volatility and the risk of decomposition at high temperatures. MALDI cannot distinguish between isomeric [...] Read more.

Aliphatic hydrocarbons (HCs) are usually analyzed by gas chromatography (GC) or matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. However, analyzing long-chain HCs by GC is difficult because of their low volatility and the risk of decomposition at high temperatures. MALDI cannot distinguish between isomeric HCs. An alternative approach based on silver ion high-performance liquid chromatography (Ag-HPLC) is shown here. The separation of HC standards and cuticular HCs was accomplished using two ChromSpher Lipids columns connected in series. A gradient elution of the analytes was optimized using mobile phases prepared from hexane (or isooctane) and acetonitrile, 2-propanol, or toluene. HCs were detected by atmospheric pressure chemical ionization mass spectrometry (APCI-MS). Good separation of the analytes according to the number of double bonds, cis/trans geometry, and position of double bonds was achieved. The retention times increased with the number of double bonds, and trans isomers eluted ahead of cis isomers. The mobile phase significantly affected the mass spectra of HCs. Depending on the mobile phase composition, deprotonated molecules, molecular ions, protonated molecules, and various solvent-related adducts of HCs were observed. The optimized Ag-HPLC/APCI-MS was applied for characterizing cuticular HCs from a flesh fly, Neobellieria bullata, and cockroach, Periplaneta americana. The method made it possible to detect a significantly higher number of HCs than previously reported for GC or MALDI-MS. Unsaturated HCs were frequently detected as isomers differing by double-bond position(s). Minor HCs with trans double bonds were found beside the prevailing cis isomers. Ag-HPLC/APCI-MS has great potential to become a new tool in chemical ecology for studying cuticular HCs. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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13 pages, 1506 KiB

Open AccessArticle

Size–Pore-Dependent Methanol Sequestration from Water–Methanol Mixtures by an Embedded Graphene Slit

by Roger Bellido-Peralta, Fabio Leoni, Carles Calero and Giancarlo Franzese

Molecules 2023, 28(9), 3697; https://doi.org/10.3390/molecules28093697 - 25 Apr 2023

Cited by 1 | Viewed by 1399

Abstract

The separation of liquid mixture components is relevant to many applications—ranging from water purification to biofuel production—and is a growing concern related to the UN Sustainable Development Goals (SDGs), such as “Clean water and Sanitation” and “Affordable and clean energy”. One promising technique [...] Read more.

The separation of liquid mixture components is relevant to many applications—ranging from water purification to biofuel production—and is a growing concern related to the UN Sustainable Development Goals (SDGs), such as “Clean water and Sanitation” and “Affordable and clean energy”. One promising technique is using graphene slit-pores as filters, or sponges, because the confinement potentially affects the properties of the mixture components in different ways, favoring their separation. However, no systematic study has shown how the size of a pore changes the thermodynamics of the surrounding mixture. Here, we focus on water–methanol mixtures and explore, using Molecular Dynamics simulations, the effects of a graphene pore, with size ranging from 6.5 to 13 Å, for three compositions: pure water, 90%–10%, and 75%–25% water–methanol. We show that tuning the pore size can change the mixture pressure, density and composition in bulk due to the size-dependent methanol sequestration within the pore. Our results can help in optimizing the graphene pore size for filtering applications. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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11 pages, 4496 KiB

Open AccessArticle

Inclusion Complexes of 3,4-Ethylenedioxythiophene with Per-Modified β- and γ-Cyclodextrins

by Aurica Farcas, Ana-Maria Resmerita, Mihaela Balan-Porcarasu, Corneliu Cojocaru, Cristian Peptu and Ion Sava

Molecules 2023, 28(8), 3404; https://doi.org/10.3390/molecules28083404 - 12 Apr 2023

Cited by 6 | Viewed by 1641

Abstract

Herein, we report the synthesis of inclusion complexes (ICs) based on 3,4-ethylenedioxythiophene (EDOT) with permethylated β-cyclodextrins (TMe-βCD) and permethylated γ-cyclodextrins (TMe-γCD) host molecules. To prove the synthesis of such ICs, molecular docking simulation, UV-vis titrations in water, ¹H-NMR, and H-H ROESY, as [...] Read more.

Herein, we report the synthesis of inclusion complexes (ICs) based on 3,4-ethylenedioxythiophene (EDOT) with permethylated β-cyclodextrins (TMe-βCD) and permethylated γ-cyclodextrins (TMe-γCD) host molecules. To prove the synthesis of such ICs, molecular docking simulation, UV-vis titrations in water, ¹H-NMR, and H-H ROESY, as well as matrix-assisted laser desorption ionization mass spectroscopy (MALDI TOF MS) and thermogravimetric analysis (TGA) were carried out on each of the EDOT∙TMe-βCD and EDOT∙TMe-γCD samples. The results of computational investigations reveal the occurrence of hydrophobic interactions, which contribute to the insertion of the EDOT guest inside the macrocyclic cavities and a better binding of the neutral EDOT to TMe-βCD. The H-H ROESY spectra show correlation peaks between H-3 and H-5 of hosts and the protons of the guest EDOT, suggesting that the EDOT molecule is included inside the cavities. The MALDI TOF MS analysis of the EDOT∙TMe-βCD solutions clearly reveals the presence of MS peaks corresponding to sodium adducts of the species associated with the complex formation. The IC preparation shows remarkable improvements in the physical properties of EDOT, rendering it a plausible alternative to increasing its aqueous solubility and thermal stability. Full article

(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)

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