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21 pages, 1603 KiB  
Article
Reactivity of Ammonia in 1,2-Addition to Group 13 Imine Analogues with G13–P–Ga Linkages: The Electronic Role of Group 13 Elements
by Zheng-Feng Zhang and Ming-Der Su
Molecules 2025, 30(15), 3222; https://doi.org/10.3390/molecules30153222 (registering DOI) - 31 Jul 2025
Viewed by 73
Abstract
Using density functional theory (M06-2X-D3/def2-TZVP), we investigated the 1,2-addition reactions of NH3 with a series of heavy imine analogues, G13=P-Rea (where G13 denotes a Group 13 element; Rea = reactant), featuring a mixed G13–P–Ga backbone. Theoretical analyses revealed that the bonding nature [...] Read more.
Using density functional theory (M06-2X-D3/def2-TZVP), we investigated the 1,2-addition reactions of NH3 with a series of heavy imine analogues, G13=P-Rea (where G13 denotes a Group 13 element; Rea = reactant), featuring a mixed G13–P–Ga backbone. Theoretical analyses revealed that the bonding nature of the G13=P moiety in G13=P-Rea molecules varies with the identity of the Group 13 center. For G13=B, Al, Ga, and In, the bonding is best described as a donor–acceptor (singlet–singlet) interaction, whereas for G13 = Tl, it is characterized by an electron-sharing (triplet–triplet) interaction. According to our theoretical studies, all G13=P-Rea species—except the Tl=P analogue—undergo 1,2-addition with NH3 under favorable energetic conditions. Energy decomposition analysis combined with natural orbitals for chemical valence (EDA–NOCV), along with frontier molecular orbital (FMO) theory, reveals that the primary bonding interaction in these reactions originates from electron donation by the lone pair on the nitrogen atom of NH3 into the vacant p-π* orbital on the G13 center. In contrast, a secondary, weaker interaction involves electron donation from the phosphorus lone pair of the G13=P-Rea species into the empty σ* orbital of the N–H bond in NH3. The calculated activation barriers are primarily governed by the deformation energy of ammonia. Specifically, as the atomic weight of the G13 element increases, the atomic radius and G13–P bond length also increase, requiring a greater distortion of the H2N–H bond to reach the transition state. This leads to a higher geometrical deformation energy of NH3, thereby increasing the activation barrier for the 1,2-addition reaction involving these Lewis base-stabilized, heavy imine-like G13=P-Rea molecules and ammonia. Full article
(This article belongs to the Special Issue Exclusive Feature Papers in Inorganic Chemistry, 3rd Edition)
9 pages, 6125 KiB  
Communication
Computational Search for a Novel Effective Ligand for Ni-Catalyzed Asymmetric Hydrogenation
by Evgeny V. Pospelov, Ivan S. Golovanov, Jianzhong Chen, Wanbin Zhang and Ilya D. Gridnev
Catalysts 2025, 15(4), 352; https://doi.org/10.3390/catal15040352 - 3 Apr 2025
Viewed by 543
Abstract
Using the DFT method, an analogue of R,R-t-Bu-BenzP* was tried as a potential ligand for Ni-catalyzed asymmetric hydrogenation. This ligand contains benzyl groups instead of the t-Bu groups in R,R-t-Bu-BenzP*. Computational results [...] Read more.
Using the DFT method, an analogue of R,R-t-Bu-BenzP* was tried as a potential ligand for Ni-catalyzed asymmetric hydrogenation. This ligand contains benzyl groups instead of the t-Bu groups in R,R-t-Bu-BenzP*. Computational results imply that the R,R-Benz-BenzP* ligand (1) is expected to provide excellent enantioselectivity in the Ni-catalyzed asymmetric hydrogenation of 1-phenylethanone oxime. The computed effectiveness of the R,R-Benz-BenzP* ligand is stipulated by its conformational flexibility, which helps stabilize the crucial transition states via a non-bonding interaction between the substrate and the catalyst. R,R-Benz-BenzP* ligands with CN- and OMe-substituted benzyl rings were also computed to possess the same effectiveness. Full article
(This article belongs to the Section Computational Catalysis)
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21 pages, 630 KiB  
Article
Polynomial Exact Schedulability and Infeasibility Test for Fixed-Priority Scheduling on Multiprocessor Platforms
by Natalia Garanina, Igor Anureev and Dmitry Kondratyev
Appl. Syst. Innov. 2025, 8(1), 15; https://doi.org/10.3390/asi8010015 - 20 Jan 2025
Viewed by 972
Abstract
In this paper, we develop an exact schedulability test and sufficient infeasibility test for fixed-priority scheduling on multiprocessor platforms. We base our tests on presenting real-time systems as a Kripke model for dynamic real-time systems with sporadic non-preemptible tasks running on a multiprocessor [...] Read more.
In this paper, we develop an exact schedulability test and sufficient infeasibility test for fixed-priority scheduling on multiprocessor platforms. We base our tests on presenting real-time systems as a Kripke model for dynamic real-time systems with sporadic non-preemptible tasks running on a multiprocessor platform and an online scheduler using global fixed priorities. This model includes states and transitions between these states, allows us to formally justify a polynomial-time algorithm for an exact schedulability test using the idea of backward reachability. Using this algorithm, we perform the exact schedulability test for the above real-time systems, in which there is one more task than the processors. The main advantage of this algorithm is its polynomial complexity, while, in general, the problem of the exact schedulability testing of real-time systems on multiprocessor platforms is NP-hard. The infeasibility test uses the same algorithm for an arbitrary task-to-processor ratio, providing a sufficient infeasibility condition: if the real-time system under test is not schedulable in some cases, the algorithm detects this. We conduct an experimental study of our algorithms on the datasets generated with different utilization values and compare them to several state-of-the-art schedulability tests. The experiments show that the performance of our algorithm exceeds the performance of its analogues while its accuracy is similar. Full article
(This article belongs to the Section Control and Systems Engineering)
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20 pages, 3666 KiB  
Article
Transition Metals Coordination by Bis-imidazole-calix[4]arene Ligands with and Without Pyrene Units Grafted at the Large Rim
by Ivana Nikšić-Franjić, Dijana Pavlović Saftić, Vilko Smrečki, Benoit Colasson, Olivia Reinaud, Ivo Piantanida and Aleksandar Višnjevac
Int. J. Mol. Sci. 2024, 25(20), 11314; https://doi.org/10.3390/ijms252011314 - 21 Oct 2024
Viewed by 1318
Abstract
Herein, the presented results show that previously studied DNA/RNA-interacting bis-imidazole-calix[4]arene systems can, in aqueous solutions, efficiently bind a series of biorelevant transition metal cations by coordination with the two imidazole arms at the small rim of their macrocyclic basket. The SCXRD and NMR [...] Read more.
Herein, the presented results show that previously studied DNA/RNA-interacting bis-imidazole-calix[4]arene systems can, in aqueous solutions, efficiently bind a series of biorelevant transition metal cations by coordination with the two imidazole arms at the small rim of their macrocyclic basket. The SCXRD and NMR results structurally characterised the complexes formed by referent bis-imidazole-calix[4]arene with Cu2+ and Zn2+. In solid-state (crystal), the bis-anilino derivative/Cu2+ complex, only upon exposure to the air, undergoes intramolecular dehydrogenative coupling of two neighbouring aniline units, yielding an azo bridge at the large rim of the calix[4]arene basket. In the biorelevant aqueous solution, the comparison of fluorometric titrations of referent calix[4]arene, with its analogues having one or two pyrene units grafted at the opposite (large) rim, revealed moderate-to-strong affinity towards transition metal cations, and, more importantly, a strong impact of pyrene on the binding affinity towards some cations. The pyrene arm(s) significantly diminished the affinity of the calix[4]arene-imidazole ligand towards Cu+ and strongly increased the affinity towards divalent Co2+ and Cd2+ cations. Moreover, the fluorometric response of some studied derivatives was strappingly sensitive to cation type. Since the counter-anion plays only a marginal role, such a change in selectivity is attributed to the intramolecular interaction of pyrene(s) with the calix[4]arene-imidazole system, sterically controlling the metal cation binding site. Full article
(This article belongs to the Special Issue Supramolecular Receptors for Cations and Anions)
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27 pages, 3084 KiB  
Article
Prospects for a Megacity Region Transition in Australia: A Preliminary Examination of Transport and Communication Drivers
by Peter Newton, James Whitten, Stephen Glackin, Margaret Reynolds and Magnus Moglia
Sustainability 2024, 16(9), 3712; https://doi.org/10.3390/su16093712 - 29 Apr 2024
Cited by 1 | Viewed by 2428
Abstract
Australian governments continue to search for a model capable of planning future urban settlements at an extended spatial scale (the mega-metropolitan region) to accommodate high population growth more sustainably. Attempts at decentralisation over the past half century have failed, as state capital cities [...] Read more.
Australian governments continue to search for a model capable of planning future urban settlements at an extended spatial scale (the mega-metropolitan region) to accommodate high population growth more sustainably. Attempts at decentralisation over the past half century have failed, as state capital cities continue to sprawl in an unsustainable manner and increase their primacy at the expense of regional cities. This paper examines how two technologies, broadband and fast rail—both infrastructures capable of re-shaping space–time relationships—could underpin a transition of Australia’s largest capital cities into megacity regions by functionally integrating regional cities into their core metropolitan agglomerations. With the Melbourne megacity region as a spatial framework, changes in population and economic development are examined for Melbourne and several regional cities in Victoria following the introduction of regional fast rail (RFR) and broadband. The impact of high-speed rail (HSR) for intercity corridors in southeast England is analysed as a possible analogue for future application in Victoria. The results revealed that RFR primarily served to extend capital city suburban development. Only HSR had the capacity to ‘punch through’ and boost growth for ‘basic’ new economy industries in ‘on-line’ urban centres in corridors linked to London. High-speed broadband proved most attractive to Melbourne’s agglomeration of high-skilled information workers. Lower speed broadband services were more uniformly taken up across all centres. This discussion speculates on the impacts of these and other green economy and digitalisation drivers on prospects for a future megacity region transition in Victoria. Full article
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26 pages, 7873 KiB  
Article
Synthesis of 4′-Thionucleoside Analogues Bearing a C2′ Stereogenic All-Carbon Quaternary Center
by Carla Eymard, Amarender Manchoju, Abir Almazloum, Starr Dostie, Michel Prévost, Mona Nemer and Yvan Guindon
Molecules 2024, 29(7), 1647; https://doi.org/10.3390/molecules29071647 - 6 Apr 2024
Cited by 1 | Viewed by 1899
Abstract
The design of novel 4′-thionucleoside analogues bearing a C2′ stereogenic all-carbon quaternary center is described. The synthesis involves a highly diastereoselective Mukaiyama aldol reaction, and a diastereoselective radical-based vinyl group transfer to generate the all-carbon stereogenic C2′ center, along with different approaches to [...] Read more.
The design of novel 4′-thionucleoside analogues bearing a C2′ stereogenic all-carbon quaternary center is described. The synthesis involves a highly diastereoselective Mukaiyama aldol reaction, and a diastereoselective radical-based vinyl group transfer to generate the all-carbon stereogenic C2′ center, along with different approaches to control the selectivity of the N-glycosidic bond. Intramolecular SN2-like cyclization of a mixture of acyclic thioaminals provided analogues with a pyrimidine nucleobase. A kinetic bias favoring cyclization of the 1′,2′-anti thioaminal furnished the desired β-D-4′-thionucleoside analogue in a 7:1 ratio. DFT calculations suggest that this kinetic resolution originates from additional steric clash in the SN2-like transition state for 1′,4′-trans isomers, causing a significant decrease in their reaction rate relative to 1′,4′-cis counterparts. N-glycosylation of cyclic glycosyl donors with a purine nucleobase enabled the formation of novel 2-chloroadenine 4′-thionucleoside analogues. These proprietary molecules and other derivatives are currently being evaluated both in vitro and in vivo to establish their biological profiles. Full article
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10 pages, 4021 KiB  
Article
Measurement of Reverse-Light-Induced Excited Spin State Trapping in Spin Crossover Systems: A Study Case with Zn1−xFex(6-mepy)3tren(PF6)2·CH3CN; x = 0.5%
by Teresa Delgado and Anne-Laure Pelé
Crystals 2024, 14(3), 210; https://doi.org/10.3390/cryst14030210 - 23 Feb 2024
Viewed by 1430
Abstract
In an attempt to better understand the physics governing the apparition of reverse-light-induced excited spin state trapping (LIESST) phenomena in spin crossover (SCO) compounds, we have studied the LIESST effect and the possibility of a reverse-LIESST effect in the SCO complex Zn1−x [...] Read more.
In an attempt to better understand the physics governing the apparition of reverse-light-induced excited spin state trapping (LIESST) phenomena in spin crossover (SCO) compounds, we have studied the LIESST effect and the possibility of a reverse-LIESST effect in the SCO complex Zn1−xFex(6-mepy)3tren(PF6)2·CH3CN, x = 0.5%. ((6-mepy)3tren = tris{4-[(6-methyl)-2-pyridyl]-3-aza-butenyl}amine)). This complex was chosen as a good candidate to show reverse-LIESST by comparison with its unsolvated analogue, since the introduction of acetonitrile in the structure leads to the stabilisation of the high-spin state and both exhibit a very abrupt thermal spin transition. Indeed, the steep thermal spin transitions of two differently polarised crystals of Zn1−xFex(6-mepy)3tren(PF6)2·CH3CN, x = 0.5% have been characterised in detail in a first step using absorption spectroscopy and no influence of the polarisation was found. These were then fitted within the mean field model to obtain the variation in the enthalpy and entropy and the critical temperatures associated with the process, which are significantly lower with respect to the unsolvated compound due to the incorporation of acetonitrile. In a second step, the light-induced low-spin-to-high-spin transition at low temperatures based on LIESST and its subsequent high-spin-to-low-spin relaxation at different temperatures were characterised by time-resolved absorption spectroscopy, with exponential behaviour in both cases. The stabilisation of the high-spin state due to the presence of acetonitrile was evidenced. Finally, light-induced high-spin-to-low-spin state transition at low temperature based on reverse-LIESST was attempted by time-resolved absorption spectroscopy but the Fe(II) concentration was too low to observe the effect. Full article
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17 pages, 4841 KiB  
Article
Rationally Designed Novel Phenyloxazoline Synthase Inhibitors: Chemical Synthesis and Biological Evaluation to Accelerate the Discovery of New Antimycobacterial Antibiotics
by Mousumi Shyam, Gourab Bhattacharje, Chris Daniel, Amrendra Kumar, Pragya Yadav, Piyali Mukherjee, Samsher Singh, Amit Kumar Das, Tadigoppula Narender, Amit Singh, Venkatesan Jayaprakash and Sanjib Bhakta
Molecules 2023, 28(24), 8115; https://doi.org/10.3390/molecules28248115 - 15 Dec 2023
Cited by 1 | Viewed by 2555
Abstract
The uncontrolled spread of drug-resistant tuberculosis (DR-TB) clinical cases necessitates the urgent discovery of newer chemotypes with novel mechanisms of action. Here, we report the chemical synthesis of rationally designed novel transition-state analogues (TSAs) by targeting the cyclization (Cy) domain of phenyloxazoline synthase [...] Read more.
The uncontrolled spread of drug-resistant tuberculosis (DR-TB) clinical cases necessitates the urgent discovery of newer chemotypes with novel mechanisms of action. Here, we report the chemical synthesis of rationally designed novel transition-state analogues (TSAs) by targeting the cyclization (Cy) domain of phenyloxazoline synthase (MbtB), a key enzyme of the conditionally essential siderophore biosynthesis pathway. Following bio-assay-guided evaluation of TSA analogues preferentially in iron-deprived and iron-rich media to understand target preferentiality against a panel of pathogenic and non-pathogenic mycobacteria strains, we identified a hit, i.e., TSA-5. Molecular docking, dynamics, and MMPBSA calculations enabled us to comprehend TSA-5’s stable binding at the active site pocket of MbtB_Cy and the results imply that the MbtB_Cy binding pocket has a strong affinity for electron-withdrawing functional groups and contributes to stable polar interactions between enzyme and ligand. Furthermore, enhanced intracellular killing efficacy (8 μg/mL) of TSA-5 against Mycobacterium aurum in infected macrophages is noted in comparison to moderate in vitro antimycobacterial efficacy (64 μg/mL) against M. aurum. TSA-5 also demonstrates whole-cell efflux pump inhibitory activity against Mycobacterium smegmatis. Identification of TSA-5 by focusing on the modular MbtB_Cy domain paves the way for accelerating novel anti-TB antibiotic discoveries. Full article
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11 pages, 1796 KiB  
Article
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 2 | Viewed by 1440
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 [NaMnII2(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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15 pages, 1167 KiB  
Article
Gamow–Teller Beta Decay and Pseudo-SU(4) Symmetry
by Piet Van Isacker, Alejandro Algora, András Vitéz-Sveiczer, Gábor Gyula Kiss, Sonja Elena Agata Orrigo, Berta Rubio and Pablo Aguilera
Symmetry 2023, 15(11), 2001; https://doi.org/10.3390/sym15112001 - 31 Oct 2023
Cited by 2 | Viewed by 1445
Abstract
We report on recent experimental results on β decay into self-conjugate (N=Z) nuclei with mass number 58A70. Super-allowed β decays from the Jπ=0+ ground state of a [...] Read more.
We report on recent experimental results on β decay into self-conjugate (N=Z) nuclei with mass number 58A70. Super-allowed β decays from the Jπ=0+ ground state of a Z=N+2 parent nucleus are to the isobaric analogue state through so-called Fermi transitions and to Jπ=1+ states by way of Gamow–Teller (GT) transitions. The operator of the latter decay is a generator of Wigner’s SU(4) algebra and as a consequence GT transitions obey selection rules associated with this symmetry. Since SU(4) is progressively broken with increasing A, mainly as a consequence of the spin–orbit interaction, this symmetry is not relevant for the nuclei considered here. We argue, however, that the pseudo-spin–orbit splitting can be small in nuclei with 58A70, in which case nuclear states exhibit an approximate pseudo-SU(4) symmetry. To test this conjecture, GT decay strength is calculated with use of a schematic Hamiltonian with pseudo-SU(4) symmetry. Some generic features of the GT β decay due to pseudo-SU(4) symmetry are pointed out. The experimentally observed GT strength indicates a restoration of pseudo-SU(4) symmetry for A=70. Full article
(This article belongs to the Special Issue Role of Symmetries in Nuclear Physics)
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13 pages, 2277 KiB  
Article
Short Fluoroalkanes Suppress a Thermally-Induced Phase Transition in a Layered Organic Crystal
by Christopher E. Marjo, Anne M. Rich, Mohan M. Bhadbhade, Saroj Bhattacharyya, Songyan Yin, David M. Miskovic, Vina R. Aldilla and Naresh Kumar
Crystals 2023, 13(10), 1425; https://doi.org/10.3390/cryst13101425 - 25 Sep 2023
Viewed by 1418
Abstract
Ensuring a consistent crystal structure over a wide temperature range can be desirable behaviour in organic devices. This study investigates a layered crystal system formed by hydrogen-bonded chloro-s-triazine rings functionalised with alkyl or fluoroalkyl chains between the layers. When substituted with [...] Read more.
Ensuring a consistent crystal structure over a wide temperature range can be desirable behaviour in organic devices. This study investigates a layered crystal system formed by hydrogen-bonded chloro-s-triazine rings functionalised with alkyl or fluoroalkyl chains between the layers. When substituted with N-propyl groups (C3), the crystal undergoes a thermally-induced phase transition where the chains are ordered and bent below 170 K and disordered and extended above 175 K. Replacement with fluorinated N-propyl chains (C3-F) produces the same layered crystal but successfully suppresses the phase transition. The hydrocarbon and fluorocarbon analogues were found to be incompatible and unable to form co-crystals from solution or with mechanical mixing. Both effects were ascribed to more attractive C-F…F-C and C-H…F-C interactions in the fluorinated analogue. Long perfluoroalkanes are well known for controlling assembly in the solid state, but this study suggests that short-chain fluoroalkanes can exert strong control over the assembly and stability of an organic crystal. Full article
(This article belongs to the Special Issue Different Kinds of Hydrogen Bonds in Crystal Structures)
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12 pages, 2583 KiB  
Article
Aurophilic Interactions of Dimeric Bisphosphine Gold(I) Complexes Pre-Organized by the Structure of the 1,5-Diaza-3,7-Diphosphacyclooctanes
by Irina R. Dayanova, Adelina I. Fayezova, Igor D. Strelnik, Igor A. Litvinov, Daut R. Islamov, Ilya E. Kolesnikov, Tatiana P. Gerasimova, Elvira I. Musina and Andrey A. Karasik
Inorganics 2022, 10(12), 224; https://doi.org/10.3390/inorganics10120224 - 25 Nov 2022
Cited by 5 | Viewed by 1987
Abstract
The dimeric gold(I) chloride and gold(I) iodide complexes ([L2Au]Cl2 and L2AuI2) on the scaffold of the cyclic bisphosphine, namely 1,5-diaza-3,7-diphosphacyclooctane containing α-phenylbenzyl (benzhydryl) substituents at the nitrogen atoms, were synthesized. The obtained complexes were isolated as [...] Read more.
The dimeric gold(I) chloride and gold(I) iodide complexes ([L2Au]Cl2 and L2AuI2) on the scaffold of the cyclic bisphosphine, namely 1,5-diaza-3,7-diphosphacyclooctane containing α-phenylbenzyl (benzhydryl) substituents at the nitrogen atoms, were synthesized. The obtained complexes were isolated as white crystalline powders. The single crystal XRD of the obtained complexes revealed the strong aurophilic interactions between two gold(I) atoms with the AuAu distance values of 2.9977(6) and 3.1680(5) Å. The comparison of the gold complexes, based on the N,N-diaryl- and N,N-dibenzhydryl substituted 1,5-diaza-3,7-diphosphacyclooctanes, allowed to reveal the strong impact of the initial heterocycle conformation on the realization of the aurophilic interactions, where the geometry of N,N-dibenzhydryl substituted 1,5-diaza-3,7-diphosphacyclooctane, is pre-organized for the intramolecular aurophilic interactions of the complexes. The obtained complexes exhibit a bluish-green phosphorescence (λem 505 (-Cl) and 530(-I)) in the solid state at room temperature, originated by the metal-halide centered transitions, which was confirmed by the TDDFT calculations. It was found that the aurophilic interactions are realized in the ground and in the triplet excited states of the complexes. The slighter change of the geometry of the N,N-dibenzhydryl substituted gold(I) iodide complexes, under the transition from the ground state to the excited state, in comparison with their N,N-diaryl substituted analogues, results in the reduced values of the Stokes shift of luminescence (ca. 150 nm vs. 175 nm). Full article
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55 pages, 21977 KiB  
Article
Common Mechanism of Activated Catalysis in P-loop Fold Nucleoside Triphosphatases—United in Diversity
by Maria I. Kozlova, Daria N. Shalaeva, Daria V. Dibrova and Armen Y. Mulkidjanian
Biomolecules 2022, 12(10), 1346; https://doi.org/10.3390/biom12101346 - 22 Sep 2022
Cited by 7 | Viewed by 4217
Abstract
To clarify the obscure hydrolysis mechanism of ubiquitous P-loop-fold nucleoside triphosphatases (Walker NTPases), we analysed the structures of 3136 catalytic sites with bound Mg-NTP complexes or their analogues. Our results are presented in two articles; here, in the second of them, we elucidated [...] Read more.
To clarify the obscure hydrolysis mechanism of ubiquitous P-loop-fold nucleoside triphosphatases (Walker NTPases), we analysed the structures of 3136 catalytic sites with bound Mg-NTP complexes or their analogues. Our results are presented in two articles; here, in the second of them, we elucidated whether the Walker A and Walker B sequence motifs—common to all P-loop NTPases—could be directly involved in catalysis. We found that the hydrogen bonds (H-bonds) between the strictly conserved, Mg-coordinating Ser/Thr of the Walker A motif ([Ser/Thr]WA) and aspartate of the Walker B motif (AspWB) are particularly short (even as short as 2.4 ångströms) in the structures with bound transition state (TS) analogues. Given that a short H-bond implies parity in the pKa values of the H-bond partners, we suggest that, in response to the interactions of a P-loop NTPase with its cognate activating partner, a proton relocates from [Ser/Thr]WA to AspWB. The resulting anionic [Ser/Thr]WA alkoxide withdraws a proton from the catalytic water molecule, and the nascent hydroxyl attacks the gamma phosphate of NTP. When the gamma-phosphate breaks away, the trapped proton at AspWB passes by the Grotthuss relay via [Ser/Thr]WA to beta-phosphate and compensates for its developing negative charge that is thought to be responsible for the activation barrier of hydrolysis. Full article
(This article belongs to the Section Enzymology)
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157 pages, 7548 KiB  
Article
Fidelity Mechanics: Analogues of the Four Thermodynamic Laws and Landauer’s Principle
by Huan-Qiang Zhou, Qian-Qian Shi and Yan-Wei Dai
Entropy 2022, 24(9), 1306; https://doi.org/10.3390/e24091306 - 15 Sep 2022
Cited by 5 | Viewed by 3263
Abstract
Fidelity mechanics is formalized as a framework for investigating critical phenomena in quantum many-body systems. Fidelity temperature is introduced for quantifying quantum fluctuations, which, together with fidelity entropy and fidelity internal energy, constitute three basic state functions in fidelity mechanics, thus enabling us [...] Read more.
Fidelity mechanics is formalized as a framework for investigating critical phenomena in quantum many-body systems. Fidelity temperature is introduced for quantifying quantum fluctuations, which, together with fidelity entropy and fidelity internal energy, constitute three basic state functions in fidelity mechanics, thus enabling us to formulate analogues of the four thermodynamic laws and Landauer’s principle at zero temperature. Fidelity flows, which are irreversible, are defined and may be interpreted as an alternative form of renormalization group flows. Thus, fidelity mechanics offers a means to characterize both stable and unstable fixed points: divergent fidelity temperature for unstable fixed points and zero-fidelity temperature and (locally) maximal fidelity entropy for stable fixed points. In addition, fidelity entropy behaves differently at an unstable fixed point for topological phase transitions and at a stable fixed point for topological quantum states of matter. A detailed analysis of fidelity mechanical-state functions is presented for six fundamental models—the quantum spin-1/2 XY model, the transverse-field quantum Ising model in a longitudinal field, the quantum spin-1/2 XYZ model, the quantum spin-1/2 XXZ model in a magnetic field, the quantum spin-1 XYZ model, and the spin-1/2 Kitaev model on a honeycomb lattice for illustrative purposes. We also present an argument to justify why the thermodynamic, psychological/computational, and cosmological arrows of time should align with each other, with the psychological/computational arrow of time being singled out as a master arrow of time. Full article
(This article belongs to the Special Issue Physical Information and the Physical Foundations of Computation)
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16 pages, 1112 KiB  
Article
A Model of Optimal Production Planning Based on the Hysteretic Demand Curve
by Mikhail E. Semenov, Sergei V. Borzunov, Peter A. Meleshenko and Alexey V. Lapin
Mathematics 2022, 10(18), 3262; https://doi.org/10.3390/math10183262 - 8 Sep 2022
Cited by 5 | Viewed by 1938
Abstract
The article considers a hysteretic model of consumer behaviour in mono-product markets. Demand generation with regard to an individual consumer is modeled using a non-ideal relay with inverted thresholds. Therefore, the sales rate is defined as an analogue of the Preisach converter. The [...] Read more.
The article considers a hysteretic model of consumer behaviour in mono-product markets. Demand generation with regard to an individual consumer is modeled using a non-ideal relay with inverted thresholds. Therefore, the sales rate is defined as an analogue of the Preisach converter. The article considers the problem of the optimal production, storage, and distribution of goods, taking into account the hysteretic nature of the demand curve. The problem is reduced to a non-classical optimal control problem with hysteretic non-linearities. The latter is solved using Pontryagin’s maximum principle. The adopted economic model is based on the binary relationship of consumers to the product: the product is bought or the product is not bought. Transitions between these states are determined within the framework of our model only by the price of the goods; therefore, only the operator of a non-ideal relay can accurately describe such a dependence. The article presents the results of computational experiments illustrating the theoretical assumptions. Full article
(This article belongs to the Special Issue Nonlinear Dynamics Systems with Hysteresis)
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