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13 pages, 1363 KiB

Open AccessArticle

Excess Enthalpies Analysis of Biofuel Components: Sunflower Oil–Alcohols Systems

by Alexandra Golikova, Anna Shasherina, Yuri Anufrikov, Georgii Misikov, Petr Kuzmenko, Alexander Smirnov, Maria Toikka and Alexander Toikka

Int. J. Mol. Sci. 2024, 25(6), 3244; https://doi.org/10.3390/ijms25063244 - 13 Mar 2024

Cited by 2 | Viewed by 1682

Abstract

This study addresses the pressing issues of energy production and consumption, in line with global sustainable development goals. Focusing on the potential of alcohols as “green” alternatives to traditional fossil fuels, especially in biofuel applications, we investigate the thermochemical properties of three alcohols [...] Read more.

This study addresses the pressing issues of energy production and consumption, in line with global sustainable development goals. Focusing on the potential of alcohols as “green” alternatives to traditional fossil fuels, especially in biofuel applications, we investigate the thermochemical properties of three alcohols (n-propanol, n-butanol, n-pentanol) blended with sunflower oil. The calorimetric analysis allows for the experimental determination of excess enthalpies in pseudo-binary mixtures at 303.15 K, revealing similarities in the trends of the curves (dependence on concentrations) but with different values for the excess enthalpies for each mixture. Despite the structural differences of the alcohols studied, the molar excess enthalpy values exhibit uniformity, suggesting consistent mixing behavior. The peak values of excess enthalpies for systems with sunflower oil and n-propanol, n-butanol and n-pentanol are, respectively, 3255.2 J/mole, 3297.4 J/mole and 3150.1 J/mole. Both the NRTL and Redlich–Kister equations show satisfactory agreement with the obtained values. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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23 pages, 9867 KiB

Open AccessArticle

The First Example of the Friedel–Crafts Cyclization Leading to (10-Hydroxy-9,10-dihydroanthr-9-yl)phosphonium Salts without the Expected Bradsher Dehydration

by Krzysztof Owsianik, Ewa Różycka-Sokołowska, Marek Koprowski, Marika Turek, Łucja Knopik, Vivek Vivek, Bogdan Dudziński and Piotr Bałczewski

Int. J. Mol. Sci. 2024, 25(3), 1741; https://doi.org/10.3390/ijms25031741 - 1 Feb 2024

Viewed by 1488

Abstract

The reaction of (ortho-acetalaryl)arylmethanols with various phosphines PR¹R²R³ (R¹ = R² = R³ = Ph; R¹ = R² = Ph, R³ = Me and R¹ = R² = [...] Read more.

The reaction of (ortho-acetalaryl)arylmethanols with various phosphines PR¹R²R³ (R¹ = R² = R³ = Ph; R¹ = R² = Ph, R³ = Me and R¹ = R² = Me, R³ = Ph) under acidic conditions (e.g., HCl, HBF₄, TsOH) unexpectedly led to the formation of (10-hydroxy-9,10-dihydroanthr-9-yl)phosphonium salts instead of the corresponding anthryl phosphonium salts. The cyclization occurred according to the Friedel–Crafts mechanism but without the usually observed Bradsher dehydration, giving cyclic products in the form of cis/trans isomers and their conformers. In case of electron-rich and less-hindered dimethylphenylphosphine, all four stereoisomers were recorded in ³¹P{¹H} NMR spectra, while for the other phosphines, only the two most stable cis/trans stereoisomers were detected. This study was supported by DFT and NCI calculations in combination with FT-IR analysis. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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9 pages, 2629 KiB

Open AccessCommunication

Enhancement of the Rates for Insertion of Zinc(II) Ions into a Cationic Porphyrin Catalyzed by Poly(glutamate)

by Roberto Zagami, Maria Angela Castriciano, Andrea Romeo and Luigi Monsù Scolaro

Int. J. Mol. Sci. 2023, 24(24), 17371; https://doi.org/10.3390/ijms242417371 - 12 Dec 2023

Cited by 1 | Viewed by 1204

Abstract

The self-assembly of porphyrins onto polyelectrolytes could lead to interesting changes in their reactivity with respect to the bulk solution. Here, we investigated the kinetics of Zn²⁺ incorporation into tetra-cationic water-soluble 5,10,15,20-tetrakis-(N-methylpyridinium-4-yl)porphyrin (TMpyP(4)) in the presence of poly(L-glutamic acid) (PGA) in a [...] Read more.

The self-assembly of porphyrins onto polyelectrolytes could lead to interesting changes in their reactivity with respect to the bulk solution. Here, we investigated the kinetics of Zn²⁺ incorporation into tetra-cationic water-soluble 5,10,15,20-tetrakis-(N-methylpyridinium-4-yl)porphyrin (TMpyP(4)) in the presence of poly(L-glutamic acid) (PGA) in a pH range from 4 to 6.5. Under these conditions, the porphyrin electrostatically interacted with the polymer, which gradually switched from an α-helical to a random coil structure. The profile of the logarithm of the observed rate constant (k_obs) versus the pH was sigmoidal with an inflection point close to the pH of the conformation transition for PGA. At a pH of 5.4, when PGA was in its highly charged random coil conformation, an almost 1000-fold increase in the reaction rates was observed. An increase in the ionic strength of the bulk solution led to a decrease in the metal insertion rates. The role of the charged matrix was explained in terms of its ability to assemble both reagents in proximity, in agreement with the theory of counter-ion condensation around polyelectrolytes in an aqueous solution. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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16 pages, 5321 KiB

Open AccessArticle

On the Importance of Halogen and Chalcogen Bonds in the Solid State of Nucleic Acids: A Combined Crystallographic and Theoretical Perspective

by María de las Nieves Piña and Antonio Bauzá

Int. J. Mol. Sci. 2023, 24(17), 13035; https://doi.org/10.3390/ijms241713035 - 22 Aug 2023

Cited by 6 | Viewed by 1362

Abstract

In this work, intra- and intermolecular halogen and chalcogen bonds (HlgBs and ChBs, respectively) present in the solid state of nucleic acids (NAs) have been studied at the RI-MP2/def2-TZVP level of theory. To achieve this, a Protein Data Bank (PDB) survey was carried [...] Read more.

In this work, intra- and intermolecular halogen and chalcogen bonds (HlgBs and ChBs, respectively) present in the solid state of nucleic acids (NAs) have been studied at the RI-MP2/def2-TZVP level of theory. To achieve this, a Protein Data Bank (PDB) survey was carried out, revealing a series of structures in which Br/I or S/Se/Te atoms belonging to nucleobases or pentose rings were involved in noncovalent interactions (NCIs) with electron-rich species. The energetics and directionality of these NCIs were rationalized through a computational study, which included the use of Molecular Electrostatic Potential (MEP) surfaces, the Quantum Theory of Atoms in Molecules (QTAIM), and Non Covalent Interaction plot (NCIplot) and Natural Bonding Orbital (NBO) techniques. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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18 pages, 397 KiB

Open AccessArticle

Improved Theory of the Effective Dipole Moments and Absolute Line Strengths of the XY₂ Asymmetric Top Molecules in the X²B₁ Doublet Electronic States

by Oleg Ulenikov, Elena Bekhtereva, Olga Gromova, Aleksei Kakaulin, Christian Sydow and Sigurd Bauerecker

Int. J. Mol. Sci. 2023, 24(16), 12734; https://doi.org/10.3390/ijms241612734 - 12 Aug 2023

Cited by 1 | Viewed by 1499

Abstract

A new effective dipole moment model for the XY₂ (

C_{2 v}

−symmetry) molecule in a doublet electronic state is derived that includes (as special cases) all currently known models of effective dipole moments for such types of molecules, and allows [...] Read more.

A new effective dipole moment model for the XY₂ (

C_{2 v}

−symmetry) molecule in a doublet electronic state is derived that includes (as special cases) all currently known models of effective dipole moments for such types of molecules, and allows us to take into account the influence of spin–rotation interactions on the effective dipole moment operator that were not considered in the preceding studies. Necessary for the analysis of absolute line strengths, the matrix elements of this dipole moment operator are derived. A comparison with the previous analog models is made and discussed. The efficiency of the obtained results is illustrated, which have been applied to a set of the “forbidden”

Δ K_{a} = 2

transitions of the

ν_{3}

band of the OClO free radical molecule. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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33 pages, 3250 KiB

Open AccessArticle

Effective Dipole Moment Model for Axially Symmetric C_3v Molecules: Application to the Precise Study of Absolute Line Strengths of the ν₆ Fundamental of CH₃³⁵Cl

by Oleg Ulenikov, Elena Bekhtereva, Olga Gromova, Anna Fomchenko, Yulia Morzhikova, Sergei Sidko, Christian Sydow and Sigurd Bauerecker

Int. J. Mol. Sci. 2023, 24(15), 12122; https://doi.org/10.3390/ijms241512122 - 28 Jul 2023

Cited by 5 | Viewed by 1955

Abstract

The effective dipole moment model for molecules of axial C

_{3 v}

symmetry is derived on the basis of the symmetry properties of a molecule which, on the one hand, is of the same order of efficiency (but much simpler and clearer in [...] Read more.

The effective dipole moment model for molecules of axial C

_{3 v}

symmetry is derived on the basis of the symmetry properties of a molecule which, on the one hand, is of the same order of efficiency (but much simpler and clearer in applications) as the analogous models derived on the basis of the irreducible tensorial sets theory, and, on the other hand, mathematically more correct in comparison with concepts like the Herman–Walles function used in the models. As an application of the general results obtained, we discuss high-resolution infrared spectra of CH

_{3}^{35}

Cl, recorded with the Zürich prototype ZP2001 (Bruker IFS125 HR) Fourier transform infrared spectrometer at a resolution of 0.001 cm

^{- 1}

and analyzed in the region of 880–1190 cm

^{- 1}

(

ν_{6}

bending fundamental centered at

ν_{0}

= 1018.070790 cm

^{- 1}

). Absolute strengths of more than 2800 transitions (2081 lines) were obtained from the fit of their shapes both with Voigt and Hartmann–Tran profiles, and parameters of the effective dipole moment of the

ν_{6}

band were determined by the computer code SYMTOMLIST (SYMmetric TOp Molecules: LIne STrengths), created on the basis of a derived theoretical model. As the first step of the analysis of the experimental data, assignments of the recorded lines were made. A total of 5124 transitions with

J^{\max}

= 68,

K^{\max}

= 21 were assigned to the

ν_{6}

band. The weighted fit of 2077 upper energy values obtained from the experimentally recorded transitions was made with a Hamiltonian which takes into account different types of ro–vibrational effects in doubly degenerate vibrational states of the

C_{3 v}

-symmetric molecule. As the result, a set of 25 fitted parameters was obtained which reproduces the initial 2077 upper “experimental” ro–vibrational energy values with a root mean square deviation

d_{rms} = 4.7 \times 10^{- 5}

cm

^{- 1}

. At the second step of the analysis, the computer code SYMTOMLIST was used for determination of the parameters of the derived effective dipole moment model. Six effective dipole moment parameters were obtained from the weighted fit procedure which reproduces absolute experimental strengths of the 2804 initial experimental transitions with a relative

d_{rms} = 3.4 %

. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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22 pages, 7587 KiB

Open AccessArticle

Effective and Selective Ru(II)-Arene Complexes Containing 4,4′-Substituted 2,2′ Bipyridine Ligands Targeting Human Urinary Bladder Cancer Cells

by Mathiyan Muralisankar, Jun-Ru Chen, Jebiti Haribabu and Shyue-Chu Ke

Int. J. Mol. Sci. 2023, 24(15), 11896; https://doi.org/10.3390/ijms241511896 - 25 Jul 2023

Cited by 8 | Viewed by 2417

Abstract

Cisplatin-based chemotherapy is a common regimen for bladder cancer, a life-threatening cancer with more than 500,000 new cases worldwide annually. Like many other metallodrugs, cisplatin causes severe side effects for its general toxicity. Organoruthenium is known for its structural stability, good anticancer activity, [...] Read more.

Cisplatin-based chemotherapy is a common regimen for bladder cancer, a life-threatening cancer with more than 500,000 new cases worldwide annually. Like many other metallodrugs, cisplatin causes severe side effects for its general toxicity. Organoruthenium is known for its structural stability, good anticancer activity, and possible low general toxicity. Here, we have prepared and characterized a series of water-soluble ruthenium-arene complexes with N,N′-chelating ligands: [Ru(II)-η⁶-arene-(4,4′-(X)₂-2,2′-bipyridine)Cl]Cl (arene = p-cymene, X = C₄H₉ (1), COOH (2), COOCH₃ (3), COOC₂H₅ (4); arene = benzene, X = C₄H₉ (5), COOCH₃ (6), COOC₂H₅ (7)). These complexes are carefully characterized using single-crystal X-ray diffraction, UV-vis, IR, ¹H NMR, and MALDI-TOF MS spectroscopy. Their DFT-calculated structural and thermodynamic properties are consistent with the experimental observations. Biophysicochemical studies of complex interaction with CTDNA and BSA supported by molecular docking simulations reveal suitable properties of 1–7 as anticancer agents. Cytotoxicities of 1–7 are evaluated on healthy human MCF-10a-breast epithelial and African green monkey Vero cells, and carcinoma human HepG-2-hepatic, T24-bladder, and EAhy-926-endothelial cells. All complexes exhibit much higher cytotoxicity for T24 than cisplatin. Particularly, 1 and 2 are also highly selective toward T24. Fluorescence imaging and flow cytometry demonstrate that 1 and 2 penetrate T24 cell membrane and induce early apoptosis at their respective IC₅₀ concentrations, which ultimately lead to cell death. Statistical analysis suggests that the order of importance for T24 cell antiproliferation is protein binding, Log p, Ru–Cl bond length, while DNA binding is the least important. This study is the first to report the anti-bladder cancer efficacy of Ru-arene-2,2′-bipyridine complexes, and may provide insights for rational design of organoruthenium drugs in the enduring search for new chemotherapeutic agents. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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11 pages, 2262 KiB

Open AccessArticle

Molecular Characteristics of Catalytic Nitrogen Removal from Coal Tar Pitch over γ-Alumina-Supported NiMo and CoMo Catalysts

by Kyoung-Hwan Choi, Dong-Jin Seo, Yu-Jin Kim, San-Seong Cho, Yu-Jin Han, Inchan Yang, Chel-Woo Kim, Kyeongseok Oh, Jung-Chul An and Joo-Il Park

Int. J. Mol. Sci. 2023, 24(14), 11793; https://doi.org/10.3390/ijms241411793 - 22 Jul 2023

Cited by 2 | Viewed by 1761

Abstract

The removal of nitrogen from coal tar pitch (CTP) through the hydrodenitrogenation (HDN) of CTP and its molecular behavior were evaluated in the presence of NiMo/γ-alumina and CoMo/γ-alumina catalysts. Fourier transform ion cyclotron resonance mass spectrometry with atmospheric pressure photoionization was used to [...] Read more.

The removal of nitrogen from coal tar pitch (CTP) through the hydrodenitrogenation (HDN) of CTP and its molecular behavior were evaluated in the presence of NiMo/γ-alumina and CoMo/γ-alumina catalysts. Fourier transform ion cyclotron resonance mass spectrometry with atmospheric pressure photoionization was used to analyze the complicated chemical classes and species of CTP and the treated products at the molecular level. Nitrogen species were qualitatively analyzed before and after hydrotreatment. A single-stage hydrotreatment with an HDN catalyst resulted in a high sulfur removal performance (85.6–94.7%) but a low nitrogen removal performance (26.8–29.2%). Based on relative abundance analyses of nitrogen and binary nitrogen species, C_cH_h-N_nS_s was the most challenging species to remove during HDN treatment. Furthermore, prior hydrodesulfurization was combined with HDN treatment, and the dual hydrotreatments yielded a significantly improved nitrogen removal performance (46.4–48.7%). Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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13 pages, 4003 KiB

Open AccessArticle

Impact of Non-Covalent Interactions of Chiral Linked Systems in Solution on Photoinduced Electron Transfer Efficiency

by Ilya M. Magin, Ivan A. Pushkin, Aleksandra A. Ageeva, Sofia O. Martianova, Nikolay E. Polyakov, Alexander B. Doktorov and Tatyana V. Leshina

Int. J. Mol. Sci. 2023, 24(11), 9296; https://doi.org/10.3390/ijms24119296 - 26 May 2023

Cited by 1 | Viewed by 1247 | Correction

Abstract

It is well-known that non-covalent interactions play an essential role in the functioning of biomolecules in living organisms. The significant attention of researchers is focused on the mechanisms of associates formation and the role of the chiral configuration of proteins, peptides, and amino [...] Read more.

It is well-known that non-covalent interactions play an essential role in the functioning of biomolecules in living organisms. The significant attention of researchers is focused on the mechanisms of associates formation and the role of the chiral configuration of proteins, peptides, and amino acids in the association. We have recently demonstrated the unique sensitivity of chemically induced dynamic nuclear polarization (CIDNP) formed in photoinduced electron transfer (PET) in chiral donor–acceptor dyads to non-covalent interactions of its diastereomers in solutions. The present study further develops the approach for quantitatively analyzing the factors that determine the association by examples of dimerization of the diastereomers with the RS, SR, and SS optical configurations. It has been shown that, under the UV irradiation of dyads, CIDNP is formed in associates, namely, homodimers (SS-SS), (SR-SR), and heterodimers (SS-SR) of diastereomers. In particular, the efficiency of PET in homo-, heterodimers, and monomers of dyads completely determines the forms of dependences of the CIDNP enhancement coefficient ratio of SS and RS, SR configurations on the ratio of diastereomer concentrations. We expect that the use of such a correlation can be useful in identifying small-sized associates in peptides, which is still a problem. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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19 pages, 4245 KiB

Open AccessArticle

Spin-Forbidden Addition of Molecular Oxygen to Stable Enol Intermediates—Decarboxylation of 2-Methyl-1-tetralone-2-carboxylic Acid

by Pablo Ortega, Sara Gil-Guerrero, Lola González-Sánchez, Cristina Sanz-Sanz and Pablo G. Jambrina

Int. J. Mol. Sci. 2023, 24(8), 7424; https://doi.org/10.3390/ijms24087424 - 18 Apr 2023

Cited by 4 | Viewed by 2521

Abstract

The deprotonation of an organic substrate is a common preactivation step for the enzymatic cofactorless addition of O

_{2}

to this substrate, as it promotes charge-transfer between the two partners, inducing intersystem crossing between the triplet and singlet states involved in the process. [...] Read more.

The deprotonation of an organic substrate is a common preactivation step for the enzymatic cofactorless addition of O

_{2}

to this substrate, as it promotes charge-transfer between the two partners, inducing intersystem crossing between the triplet and singlet states involved in the process. Nevertheless, the spin-forbidden addition of O

_{2}

to uncharged ligands has also been observed in the laboratory, and the detailed mechanism of how the system circumvents the spin-forbiddenness of the reaction is still unknown. One of these examples is the cofactorless peroxidation of 2-methyl-3,4-dihydro-1-naphthol, which will be studied computationally using single and multi-reference electronic structure calculations. Our results show that the preferred mechanism is that in which O

_{2}

picks a proton from the substrate in the triplet state, and subsequently hops to the singlet state in which the product is stable. For this reaction, the formation of the radical pair is associated with a higher barrier than that associated with the intersystem crossing, even though the absence of the negative charge leads to relatively small values of the spin-orbit coupling. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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13 pages, 2633 KiB

Open AccessArticle

High-Performance Potassium-Selective Biosensor Platform Based on Resistive Coupling of a-IGZO Coplanar-Gate Thin-Film Transistor

by Tae-Hwan Hyun and Won-Ju Cho

Int. J. Mol. Sci. 2023, 24(7), 6164; https://doi.org/10.3390/ijms24076164 - 24 Mar 2023

Cited by 4 | Viewed by 2688

Abstract

The potassium (K⁺) ion is an essential mineral for balancing body fluids and electrolytes in biological systems and regulating bodily function. It is associated with various disorders. Given that it exists at a low concentration in the human body and should [...] Read more.

The potassium (K⁺) ion is an essential mineral for balancing body fluids and electrolytes in biological systems and regulating bodily function. It is associated with various disorders. Given that it exists at a low concentration in the human body and should be maintained at a precisely stable level, the development of highly efficient potassium-selective sensors is attracting considerable interest in the healthcare field. Herein, we developed a high-performance, potassium-selective field-effect transistor-type biosensor platform based on an amorphous indium gallium zinc oxide coplanar-gate thin-film transistor using a resistive coupling effect with an extended gate containing a potassium-selective membrane. The proposed sensor can detect potassium in KCl solutions with a high sensitivity of 51.9 mV/dec while showing a low sensitivity of <6.6 mV/dec for NaCl, CaCl₂, and pH buffer solutions, indicating its high selectivity to potassium. Self-amplification through the resistive-coupling effect enabled an even greater potassium sensitivity of 597.1 mV/dec. Additionally, we ensured the stability and reliability of short- and long-term detection through the assessment of non-ideal behaviors, including hysteresis and drift effects. Therefore, the proposed potassium-sensitive biosensor platform is applicable to high-performance detection in a living body, with high sensitivity and selectivity for potassium. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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16 pages, 5815 KiB

Open AccessArticle

Secondary and Topological Structural Merge Prediction of Alpha-Helical Transmembrane Proteins Using a Hybrid Model Based on Hidden Markov and Long Short-Term Memory Neural Networks

by Ting Gao, Yutong Zhao, Li Zhang and Han Wang

Int. J. Mol. Sci. 2023, 24(6), 5720; https://doi.org/10.3390/ijms24065720 - 16 Mar 2023

Cited by 3 | Viewed by 2132

Abstract

Alpha-helical transmembrane proteins (αTMPs) play essential roles in drug targeting and disease treatments. Due to the challenges of using experimental methods to determine their structure, αTMPs have far fewer known structures than soluble proteins. The topology of transmembrane proteins (TMPs) can determine the [...] Read more.

Alpha-helical transmembrane proteins (αTMPs) play essential roles in drug targeting and disease treatments. Due to the challenges of using experimental methods to determine their structure, αTMPs have far fewer known structures than soluble proteins. The topology of transmembrane proteins (TMPs) can determine the spatial conformation relative to the membrane, while the secondary structure helps to identify their functional domain. They are highly correlated on αTMPs sequences, and achieving a merge prediction is instructive for further understanding the structure and function of αTMPs. In this study, we implemented a hybrid model combining Deep Learning Neural Networks (DNNs) with a Class Hidden Markov Model (CHMM), namely HDNNtopss. DNNs extract rich contextual features through stacked attention-enhanced Bidirectional Long Short-Term Memory (BiLSTM) networks and Convolutional Neural Networks (CNNs), and CHMM captures state-associative temporal features. The hybrid model not only reasonably considers the probability of the state path but also has a fitting and feature-extraction capability for deep learning, which enables flexible prediction and makes the resulting sequence more biologically meaningful. It outperforms current advanced merge-prediction methods with a Q4 of 0.779 and an MCC of 0.673 on the independent test dataset, which have practical, solid significance. In comparison to advanced prediction methods for topological and secondary structures, it achieves the highest topology prediction with a Q2 of 0.884, which has a strong comprehensive performance. At the same time, we implemented a joint training method, Co-HDNNtopss, and achieved a good performance to provide an important reference for similar hybrid-model training. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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21 pages, 4526 KiB

Open AccessArticle

A Comprehensive Ab Initio Study of Halogenated A···U and G···C Base Pair Geometries and Energies

by Rosa M. Gomila, Antonio Frontera and Antonio Bauzá

Int. J. Mol. Sci. 2023, 24(6), 5530; https://doi.org/10.3390/ijms24065530 - 14 Mar 2023

Cited by 4 | Viewed by 1988

Abstract

Unraveling the binding preferences involved in the formation of a supramolecular complex is key to properly understand molecular recognition and aggregation phenomena, which are of pivotal importance to biology. The halogenation of nucleic acids has been routinely carried out for decades to assist [...] Read more.

Unraveling the binding preferences involved in the formation of a supramolecular complex is key to properly understand molecular recognition and aggregation phenomena, which are of pivotal importance to biology. The halogenation of nucleic acids has been routinely carried out for decades to assist in their X-ray diffraction analysis. The incorporation of a halogen atom on a DNA/RNA base not only affected its electronic distribution, but also expanded the noncovalent interactions toolbox beyond the classical hydrogen bond (HB) by incorporating the halogen bond (HalB). In this regard, an inspection of the Protein Data Bank (PDB) revealed 187 structures involving halogenated nucleic acids (either unbound or bound to a protein) where at least 1 base pair (BP) exhibited halogenation. Herein, we were interested in disclosing the strength and binding preferences of halogenated A···U and G···C BPs, which are predominant in halogenated nucleic acids. To achieve that, computations at the RI-MP2/def2-TZVP level of theory together with state of the art theoretical modeling tools (including the computation of molecular electrostatic potential (MEP) surfaces, the quantum theory of “Atoms in Molecules” (QTAIM) and the non-covalent interactions plot (NCIplot) analyses) allowed for the characterization of the HB and HalB complexes studied herein. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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10 pages, 1480 KiB

Open AccessArticle

Quantum-Chemical Prediction of Molecular and Electronic Structure of Carbon-Nitrogen Chemical Compound with Unusual Ratio Atoms: C(N₂₀)

by Oleg V. Mikhailov and Denis V. Chachkov

Int. J. Mol. Sci. 2023, 24(6), 5172; https://doi.org/10.3390/ijms24065172 - 8 Mar 2023

Cited by 3 | Viewed by 1992

Abstract

Using various versions of quantum-chemical calculation, namely four versions of density functional theory (DFT), (DFT B3PW91/TZVP, DFT M06/TZVP, DFT B3PW91/Def2TZVP, and DFT M06/Def2TZVP) and two versions of the MP method (MP2/TZVP and MP3/TZVP), the existence possibility of the carbon-nitrogen-containing compound having an unusual [...] Read more.

Using various versions of quantum-chemical calculation, namely four versions of density functional theory (DFT), (DFT B3PW91/TZVP, DFT M06/TZVP, DFT B3PW91/Def2TZVP, and DFT M06/Def2TZVP) and two versions of the MP method (MP2/TZVP and MP3/TZVP), the existence possibility of the carbon-nitrogen-containing compound having an unusual M: nitrogen ratio of 1:20, unknown for these elements at present, was shown. Structural parameters data are presented; it was noted that, as may be expected, CN₄ grouping has practically a tetrahedral structure, and the chemical bond lengths formed by nitrogen atoms and a carbon atom in the frameworks of each of the calculation methods indicated above are equal to each other. Thermodynamical parameters, NBO analysis data, and HOMO/LUMO images for this compound are also presented. A good agreement between the calculated data obtained using the above three quantum-chemical methods was noticed, too. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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13 pages, 4839 KiB

Open AccessArticle

3D Characterization of the Molecular Neighborhood of ^•OH Radical in High Temperature Water by MD Simulation and Voronoi Polyhedra

by Lukasz Kazmierczak, Joanna Szala-Rearick and Dorota Swiatla-Wojcik

Int. J. Mol. Sci. 2023, 24(4), 3294; https://doi.org/10.3390/ijms24043294 - 7 Feb 2023

Viewed by 1822

Abstract

Understanding the properties of the ^•OH radical in aqueous environments is essential for biochemistry, atmospheric chemistry, and the development of green chemistry technologies. In particular, the technological applications involve knowledge of microsolvation of the ^•OH radical in high temperature water. In [...] Read more.

Understanding the properties of the ^•OH radical in aqueous environments is essential for biochemistry, atmospheric chemistry, and the development of green chemistry technologies. In particular, the technological applications involve knowledge of microsolvation of the ^•OH radical in high temperature water. In this study, the classical molecular dynamics (MD) simulation and the technique based on the construction of Voronoi polyhedra were used to provide 3D characteristics of the molecular vicinity of the aqueous hydroxyl radical (^•OH_aq). The statistical distribution functions of metric and topological features of solvation shells represented by the constructed Voronoi polyhedra are reported for several thermodynamic states of water, including the pressurized high-temperature liquid and supercritical fluid. Calculations showed a decisive influence of the water density on the geometrical properties of the ^•OH solvation shell in the sub- and supercritical region: with the decreasing density, the span and asymmetry of the solvation shell increase. We also showed that the 1D analysis based on the oxygen–oxygen radial distribution functions (RDFs) overestimates the solvation number of ^•OH and insufficiently reflects the influence of transformations in the hydrogen-bonded network of water on the structure of the solvation shell. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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18 pages, 7249 KiB

Open AccessArticle

Microenvironmental Impact on InP/ZnS-Based Quantum Dots in In Vitro Models and in Living Cells: Spectrally- and Time-Resolved Luminescence Analysis

by Ilia Litvinov, Anna Salova, Nikolay Aksenov, Elena Kornilova and Tatiana Belyaeva

Int. J. Mol. Sci. 2023, 24(3), 2699; https://doi.org/10.3390/ijms24032699 - 31 Jan 2023

Cited by 4 | Viewed by 2358

Abstract

Quantum dots (QDs) have attracted great attention as tools for theranostics that combine the possibility of simultaneous biological target visualization and medicine delivery. Here, we address whether core/shell InP/ZnS QDs (InP-QDs) may be an alternative to toxic Cd-based QDs. We analyze InP-QD photophysical [...] Read more.

Quantum dots (QDs) have attracted great attention as tools for theranostics that combine the possibility of simultaneous biological target visualization and medicine delivery. Here, we address whether core/shell InP/ZnS QDs (InP-QDs) may be an alternative to toxic Cd-based QDs. We analyze InP-QD photophysical characteristics in cell culture medium, salt solutions, and directly in the cells. It was demonstrated that InP-QDs were internalized into endolysosomes in HeLa and A549 cells with dynamics similar to Cd-based QDs of the same design, but the two cell lines accumulated them with different efficiencies. InP-QDs were reliably detected in the endosomes despite their low quantum yields. Cell culture medium efficiently decreased the InP-QD photoluminescence lifetime by 50%, acidic pH (4.0) had a moderate effect (20–25% reduction), and quenching by salt solutions typical of intra-endosomal medium composition resulted in a decrease of about 10–15%. The single-vesicle fluorescence-lifetime imaging microscopy analysis of QDs inside and outside the cells shows that the scatter between endosomes in the same cell can be significant, which indicates the complex impact of the abovementioned factors on the state of InP-QDs. The PI test and MTT test demonstrate that InP-QDs are toxic for both cell lines at concentrations higher than 20 nM. Possible reasons for InP-QD toxicity are discussed. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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17 pages, 4845 KiB

Open AccessArticle

Combined Fluorescence Fluctuation and Spectrofluorometric Measurements Reveal a Red-Shifted, Near-IR Emissive Photo-Isomerized Form of Cyanine 5

by Elin Sandberg, Joachim Piguet, Haichun Liu and Jerker Widengren

Int. J. Mol. Sci. 2023, 24(3), 1990; https://doi.org/10.3390/ijms24031990 - 19 Jan 2023

Cited by 6 | Viewed by 1985

Abstract

Cyanine fluorophores are extensively used in fluorescence spectroscopy and imaging. Upon continuous excitation, especially at excitation conditions used in single-molecule and super-resolution experiments, photo-isomerized states of cyanines easily reach population probabilities of around 50%. Still, effects of photo-isomerization are largely ignored in such [...] Read more.

Cyanine fluorophores are extensively used in fluorescence spectroscopy and imaging. Upon continuous excitation, especially at excitation conditions used in single-molecule and super-resolution experiments, photo-isomerized states of cyanines easily reach population probabilities of around 50%. Still, effects of photo-isomerization are largely ignored in such experiments. Here, we studied the photo-isomerization of the pentamethine cyanine 5 (Cy5) by two similar, yet complementary means to follow fluorophore blinking dynamics: fluorescence correlation spectroscopy (FCS) and transient-state (TRAST) excitation–modulation spectroscopy. Additionally, we combined TRAST and spectrofluorimetry (spectral-TRAST), whereby the emission spectra of Cy5 were recorded upon different rectangular pulse-train excitations. We also developed a framework for analyzing transitions between multiple emissive states in FCS and TRAST experiments, how the brightness of the different states is weighted, and what initial conditions that apply. Our FCS, TRAST, and spectral-TRAST experiments showed significant differences in dark-state relaxation amplitudes for different spectral detection ranges, which we attribute to an additional red-shifted, emissive photo-isomerized state of Cy5, not previously considered in FCS and single-molecule experiments. The photo-isomerization kinetics of this state indicate that it is formed under moderate excitation conditions, and its population and emission may thus deserve also more general consideration in fluorescence imaging and spectroscopy experiments. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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19 pages, 2297 KiB

Open AccessArticle

Regioselective Cycloaddition of Nitrile Imines to 5-Methylidene-3-phenyl-hydantoin: Synthesis and DFT Calculations

by Maria E. Filkina, Daria N. Baray, Elena K. Beloglazkina, Yuri K. Grishin, Vitaly A. Roznyatovsky and Maxim E. Kukushkin

Int. J. Mol. Sci. 2023, 24(2), 1289; https://doi.org/10.3390/ijms24021289 - 9 Jan 2023

Cited by 13 | Viewed by 3102

Abstract

Nitrile imine cycloaddition to hydantoins containing an exocyclic C=C double bond has been previously described in a very limited number of examples. In this work, regioselective synthesis of spiro-pyrazoline-imidazolidine-2,4-diones based on a 1,3-dipolar cycloaddition reaction of nitrile imines to 5-methylidene-3-phenyl-hydantoin have been proposed. [...] Read more.

Nitrile imine cycloaddition to hydantoins containing an exocyclic C=C double bond has been previously described in a very limited number of examples. In this work, regioselective synthesis of spiro-pyrazoline-imidazolidine-2,4-diones based on a 1,3-dipolar cycloaddition reaction of nitrile imines to 5-methylidene-3-phenyl-hydantoin have been proposed. It was found that, regardless of the nature of the aryl substituents at the terminal C and N atoms of the C-N-N fragment of nitrile imine (electron donor or electron acceptor), cycloaddition to the 5-methylidenhydantoin exocyclic C=C bond proceeds regioselectively, and the terminal nitrogen atom of the nitrile imine connects to the more sterically hindered carbon atom of the double bond, which leads to the formation of a 5-disubstituted pyrazoline ring. The observed cycloaddition regioselectivity was rationalized using DFT calculations of frontier molecular orbital interactions, global CDFT reactivity indices, and minimum energy paths. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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23 pages, 4864 KiB

Open AccessReview

Systematic Development of Vanadium Catalysts for Sustainable Epoxidation of Small Alkenes and Allylic Alcohols

by José Ferraz-Caetano, Filipe Teixeira and Maria Natália Dias Soeiro Cordeiro

Int. J. Mol. Sci. 2023, 24(15), 12299; https://doi.org/10.3390/ijms241512299 - 1 Aug 2023

Cited by 5 | Viewed by 2973

Abstract

The catalytic epoxidation of small alkenes and allylic alcohols includes a wide range of valuable chemical applications, with many works describing vanadium complexes as suitable catalysts towards sustainable process chemistry. But, given the complexity of these mechanisms, it is not always easy to [...] Read more.

The catalytic epoxidation of small alkenes and allylic alcohols includes a wide range of valuable chemical applications, with many works describing vanadium complexes as suitable catalysts towards sustainable process chemistry. But, given the complexity of these mechanisms, it is not always easy to sort out efficient examples for streamlining sustainable processes and tuning product optimization. In this review, we provide an update on major works of tunable vanadium-catalyzed epoxidations, with a focus on sustainable optimization routes. After presenting the current mechanistic view on vanadium catalysts for small alkenes and allylic alcohols’ epoxidation, we argue the key challenges in green process development by highlighting the value of updated kinetic and mechanistic studies, along with essential computational studies. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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23 pages, 2461 KiB

Open AccessReview

Recent Advances in THz Detection of Water

by Hongyi Ge, Zhenyu Sun, Yuying Jiang, Xuyang Wu, Zhiyuan Jia, Guangyuan Cui and Yuan Zhang

Int. J. Mol. Sci. 2023, 24(13), 10936; https://doi.org/10.3390/ijms241310936 - 30 Jun 2023

Cited by 21 | Viewed by 5780

Abstract

The frequency range of terahertz waves (THz waves) is between 0.1 and 10 THz and they have properties such as low energy, penetration, transients, and spectral fingerprints, which are especially sensitive to water. Terahertz, as a frontier technology, have great potential in interpreting [...] Read more.

The frequency range of terahertz waves (THz waves) is between 0.1 and 10 THz and they have properties such as low energy, penetration, transients, and spectral fingerprints, which are especially sensitive to water. Terahertz, as a frontier technology, have great potential in interpreting the structure of water molecules and detecting biological water conditions, and the use of terahertz technology for water detection is currently frontier research, which is of great significance. Firstly, this paper introduces the theory of terahertz technology and summarizes the current terahertz systems used for water detection. Secondly, an overview of theoretical approaches, such as the relaxation model and effective medium theory related to water detection, the relationship between water molecular networks and terahertz spectra, and the research progress of the terahertz detection of water content and water distribution visualization, are elaborated. Finally, the challenge and outlook of applications related to the terahertz wave detection of water are discussed. The purpose of this paper is to explore the research domains on water and its related applications using terahertz technology, as well as provide a reference for innovative applications of terahertz technology in moisture detection. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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24 pages, 2912 KiB

Open AccessReview

Recent Advances in the Preparation of Delivery Systems for the Controlled Release of Scents

by Adrian Saura-Sanmartin and Laura Andreu-Ardil

Int. J. Mol. Sci. 2023, 24(5), 4685; https://doi.org/10.3390/ijms24054685 - 28 Feb 2023

Cited by 9 | Viewed by 4968

Abstract

Scents are volatile compounds highly employed in a wide range of manufactured items, such as fine perfumery, household products, and functional foods. One of the main directions of the research in this area aims to enhance the longevity of scents by designing efficient [...] Read more.

Scents are volatile compounds highly employed in a wide range of manufactured items, such as fine perfumery, household products, and functional foods. One of the main directions of the research in this area aims to enhance the longevity of scents by designing efficient delivery systems to control the release rate of these volatile molecules and also increase their stability. Several approaches to release scents in a controlled manner have been developed in recent years. Thus, different controlled release systems have been prepared, including polymers, metal–organic frameworks and mechanically interlocked systems, among others. This review is focused on the preparation of different scaffolds to accomplish a slow release of scents, by pointing out examples reported in the last five years. In addition to discuss selected examples, a critical perspective on the state of the art of this research field is provided, comparing the different types of scent delivery systems. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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