共查询到20条相似文献,搜索用时 15 毫秒
1.
Lars Esser Roberto Macchieraldo Roman Elfgen Melanie Sieland Bernd Michael Smarsly Barbara Kirchner 《Molecules (Basel, Switzerland)》2021,26(1)
To gain a deeper understanding of the TiCl solvation effects in multi-component ionic liquids, we performed ab initio molecular dynamics simulations of 1-butyl-3-methylimidazolium [CCIm], tetrafluoroborate [BF], chloride [Cl] both with and without water and titanium tetrachloride TiCl. Complex interactions between cations and anions are observed in all investigated systems. By further addition of water and TiCl this complex interaction network is extended. Observations of the radial distribution functions and number integrals show that water and TiCl not only compete with each other to interact mainly with [Cl], which strongly influences the cation-[BF] interaction, but also interact with each other, which leads to the fact that in certain systems the cation-anion interaction is enhanced. Further investigations of the Voronoi polyhedra analysis have demonstrated that water has a greater impact on the nanosegregated system than TiCl which is also due to the fact of the shear amount of water relative to all other components and its higher mobility compared to TiCl. Overall, the polar network of the IL mixture collapses by including water and TiCl. In the case of [Cl] chloride enters the water continuum, while [BF] remains largely unaffected, which deeply affects the interaction of the ionic liquid (IL) network. 相似文献
2.
Massimiliano Bartolomei Paul Martini Ricardo Prez de Tudela Toms Gonzlez-Lezana Marta I. Hernndez Jos Campos-Martínez Javier Hernndez-Rojas Jos Bretn Paul Scheier 《Molecules (Basel, Switzerland)》2021,26(12)
We present a combined experimental and theoretical investigation on Ca ions in helium droplets, HeCa. The clusters have been formed in the laboratory by means of electron-impact ionization of Ca-doped helium nanodroplets. Energies and structures of such complexes have been computed using various approaches such as path integral Monte Carlo, diffusion Monte Carlo and basin-hopping methods. The potential energy functions employed in these calculations consist of analytical expressions following an improved Lennard-Jones formula whose parameters are fine-tuned by exploiting ab initio estimations. Ion yields of HeCa -obtained via high-resolution mass spectrometry- generally decrease with N with a more pronounced drop between and , the computed quantum HeCa evaporation energies resembling this behavior. The analysis of the energies and structures reveals that covering Ca with 17 He atoms leads to a cluster with one of the smallest energies per atom. As new atoms are added, they continue to fill the first shell at the expense of reducing its stability, until , which corresponds to the maximum number of atoms in that shell. Behavior of the evaporation energies and radial densities suggests liquid-like cluster structures. 相似文献
3.
Ken Taguchi Akihiko Toda Hironori Hondoh Satoru Ueno Kiyotaka Sato 《Molecules (Basel, Switzerland)》2021,26(1)
The crystallization behavior of the metastable form of triacylglycerols (TAGs) plays a critical role as a precursor for the crystallization of more stable and forms for various applications in food and pharmaceutical products. However, precise analysis of the crystallization kinetics of has not been performed, likely due to its rapid and complex behavior. This paper presents the observation results of the initial stages of the isothermal crystallization kinetics of forms of 1,3-dipalmitoyl-2-oleoyl-glycerol (POP), 1,2-dipalmitoyl-3-oleoyl-rac-glycerol (rac-PPO), and molecular compound (MC) crystals of a POP/rac-PPO (1/1) mixture (MC) using synchrotron radiation time-resolved X-ray diffraction and polarized optical microscopy. In all the TAGs, crystals with a worm-like morphology started to grow rapidly in the first stage. Then, the crystals slowly transformed into more stable forms in different manners for different TAG samples. In POP, the conversion was simple, as the -2 form transformed into -3, whereas in rac-PPO, the lamellar distance values of the -2 form continuously decreased with time and changed into the -3 form. In the MC crystals, in contrast, separate crystallization of -2 of a rac-PPO fraction initially occurred, followed by the crystallization of -2 of POP, and the two forms merged into -2 of MC. This separate crystallization was caused by large differences in the crystallization kinetics of the forms of POP and rac-PPO. 相似文献
4.
Mohamed Ahmed Khaireh Marie Angot Clara Cilindre Grard Liger-Belair David A. Bonhommeau 《Molecules (Basel, Switzerland)》2021,26(6)
The diffusion of carbon dioxide (CO) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue. 相似文献
5.
Diego T. Gomez Lawrence R. Pratt David M. Rogers Susan B. Rempe 《Molecules (Basel, Switzerland)》2021,26(11)
With a longer-term goal of addressing the comparative behavior of the aqueous halides F, Cl, Br, and I on the basis of quasi-chemical theory (QCT), here we study structures and free energies of hydration clusters for those anions. We confirm that energetically optimal clusters, with X = Cl, Br, and I, exhibit surface hydration structures. Computed free energies, based on optimized surface hydration structures utilizing a harmonic approximation, typically (but not always) disagree with experimental free energies. To remedy the harmonic approximation, we utilize single-point electronic structure calculations on cluster geometries sampled from an AIMD (ab initio molecular dynamics) simulation stream. This rough-landscape procedure is broadly satisfactory and suggests unfavorable ligand crowding as the physical effect addressed. Nevertheless, this procedure can break down when , with the characteristic discrepancy resulting from a relaxed definition of clustering in the identification of clusters, including ramified structures natural in physical cluster theories. With ramified structures, the central equation for the present rough-landscape approach can acquire some inconsistency. Extension of these physical cluster theories in the direction of QCT should remedy that issue, and should be the next step in this research direction. 相似文献
6.
The S2 state produces two basic electron paramagnetic resonance signal types due to the manganese cluster in oxygen-evolving complex, which are influenced by the solvents, and cryoprotectant added to the photosystem II samples. It is presumed that a single manganese center oxidation occurs on S1 → S2 state transition. The S2 state has readily visible multiline and electron paramagnetic resonance signals and hence it has been the most studied of all the Kok cycle intermediates due to the ease of experimental preparation and stability. The S2 state was studied using electron paramagnetic resonance spectroscopy at X-band frequencies. The aim of this study was to determine the spin states of the signal. The multiline signal was observed to arise from a ground state spin ½ centre while the 4.1 signal generated at ≈140 K NIR illumination was proposed to arise from a spin center with rhombic distortion. The ‘ground’ state 4.1 signal was generated solely or by conversion from the multiline. The data analysis methods used involved numerical simulations of the experimental spectra on relevant models of the oxygen-evolving complex cluster. A strong focus in this paper was on the ‘ground’ state 4.1 signal, whether it is a rhombic spin state signal or an axial spin state signal. The data supported an X-band CW-EPR-generated 4.1 signal as originating from a near rhombic spin 5/2 of the S2 state of the PSII manganese cluster. 相似文献
7.
Water borane (BHOH) and borinic acid (BHOH) have been proposed as intermediates along the pathway of hydrogen generation from simple reactants: water and borane. However, the vibrational spectra for neither water borane nor borinic acid has been investigaged experimentally due to the difficulty of isolating them in the gas phase, making accurate quantum chemical predictions for such properties the most viable means of their determination. This work presents theoretical predictions of the full rotational and fundamental vibrational spectra of these two potentially application-rich molecules using quartic force fields at the CCSD(T)-F12b/cc-pCVTZ-F12 level with additional corrections included for the effects of scalar relativity. This computational scheme is further benchmarked against the available gas-phase experimental data for the related borane and HBO molecules. The differences are found to be within 3 cm for the fundamental vibrational frequencies and as close as 15 MHz in the and principal rotational constants. Both BHOH and BHOH have multiple vibrational modes with intensities greater than 100 km mol, namely and in BHOH, and , , , , and in BHOH. Finally, BHOH has a large dipole moment of 4.24 D, which should enable it to be observable by rotational spectroscopy, as well. 相似文献
8.
We present a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics–statistical approach for the interpretation of nuclear magnetic resonance (NMR) chemical shift patterns in phycocyanobilin (PCB). These were originally associated with colour tuning upon photoproduct formation in red/green-absorbing cyanobacteriochrome AnPixJg2 and red/far-red-absorbing phytochrome Cph12. We pursue an indirect approach without computation of the absorption frequencies since the molecular geometry of cofactor and protein are not accurately known. Instead, we resort to a heuristic determination of the conjugation length in PCB through the experimental NMR chemical shift patterns, supported by quantum chemical calculations. We have found a characteristic correlation pattern of C chemical shifts to specific bond orders within the -conjugated system, which rests on the relative position of carbon atoms with respect to electron-withdrawing groups and the polarisation of covalent bonds. We propose the inversion of this regioselective relationship using multivariate statistics and to apply it to the known experimental NMR chemical shifts in order to predict changes in the bond alternation pattern. Therefrom the extent of electronic conjugation, and eventually the change in absorption frequency, can be derived. In the process, the consultation of explicit mesomeric formulae plays an important role to qualitatively account for possible conjugation scenarios of the chromophore. While we are able to consistently associate the NMR chemical shifts with hypsochromic and bathochromic shifts in the P and P, our approach represents an alternative method to increase the explanatory power of NMR spectroscopic data in proteins. 相似文献
9.
We study the magnetic properties of the erbium based compounds, Na[Er(WO)] and [(Pc)Er{Pc{N(CH)}}], in the framework of an effective spin exchange model involving delocalized electrons occupying molecular orbitals. The calculations successfully reproduce the experimental data available in the literature for the magnetic spectrum, magnetization and molar susceptibility in dc and ac fields. Owing to their similar molecular geometry, the compounds’ magnetic behaviors are interpreted in terms of the same set of active orbitals and thus the same effective spin coupling scheme. For all three complexes, the model predicts a prompt change in the ground state from a Kramer’s doublet at zero fields to a fully polarized quartet one brought about by the action of an external magnetic field without Zeeman splitting. This alteration is attributed to the enhancement of the effect of orbital interactions over the spin exchange as the magnitude of the external magnetic field increases. 相似文献
10.
Faranak Bahrami Mykola Abramchuk Oleg Lebedev Fazel Tafti 《Molecules (Basel, Switzerland)》2022,27(3)
Nearly two decades ago, Alexei Kitaev proposed a model for spin- particles with bond-directional interactions on a two-dimensional honeycomb lattice which had the potential to host a quantum spin-liquid ground state. This work initiated numerous investigations to design and synthesize materials that would physically realize the Kitaev Hamiltonian. The first generation of such materials, such as NaIrO, -LiIrO, and -RuCl, revealed the presence of non-Kitaev interactions such as the Heisenberg and off-diagonal exchange. Both physical pressure and chemical doping were used to tune the relative strength of the Kitaev and competing interactions; however, little progress was made towards achieving a purely Kitaev system. Here, we review the recent breakthrough in modifying Kitaev magnets via topochemical methods that has led to the second generation of Kitaev materials. We show how structural modifications due to the topotactic exchange reactions can alter the magnetic interactions in favor of a quantum spin-liquid phase. 相似文献
11.
Thymine photochemistry is important for understanding DNA photodamage. In the gas phase, thymine undergoes a fast non-radiative decay from S to S . In the S state, it gets trapped for several picoseconds until returning to the ground-state S . Here, we explore the electrostatic effects of nanomeric droplets of methanol and water on the excited states of thymine. For this purpose, we develop and implement an electrostatic embedding TD-DFT/MM method based on a QM/MM coupling defined through electrostatic potential fitting charges. We show that both in methanol and water, the mechanism is similar to the gas phase. The solvent molecules participate in defining the branching plane of S /S intersection and have a negligible effect on the S /S intersection. Despite the wrong topology of the ground/excited state intersections, electrostatic embedding TD-DFT/MM allows for a fast exploration of the potential energy surfaces and a qualitative picture of the photophysics of thymine in solvent droplets. 相似文献
12.
Li-rich and catalytically active - (x = 1.48) was investigated as a cathode for its heterogeneous charge transfer kinetics. Using a specially designed two-electrode system lithium half cell, Butler–Volmer analysis was performed, and Raman spectra were acquired in 18 mV intervals. A direct correlation was observed between the Raman shift of the active modes ,, , and , and the development of the Faraday current at the working electrode. The Raman intensity and the Raman shift were implemented to replace the current in a Tafel plot used for the analysis of Butler–Volmer kinetics. Striking similarities in the charge transfer proportionality constants were found for current and Raman-based analysis. The potential of this new method of Raman-aided electrochemical detection at the diffraction limit is discussed. 相似文献
13.
Noncovalent interactions play a pivotal role in regulating protein conformation, stability and dynamics. Among the quantum mechanical (QM) overlap-based noncovalent interactions, is the best understood with studies ranging from small molecules to -turns of model proteins such as GB1. However, these investigations do not explore the interplay between multiple overlap interactions in contributing to local structure and stability. In this work, we identify and characterize all noncovalent overlap interactions in the -turn, an important secondary structural element that facilitates the folding of a polypeptide chain. Invoking a QM framework of natural bond orbitals, we demonstrate the role of several additional interactions such as and that are energetically comparable to or larger than . We find that these interactions are sensitive to changes in the side chain of the residues in the -turn of GB1, suggesting that the may not be the only component in dictating -turn conformation and stability. Furthermore, a database search of and in the PDB reveals that they are prevalent in most proteins and have significant interaction energies (∼1 kcal/mol). This indicates that all overlap interactions must be taken into account to obtain a comprehensive picture of their contributions to protein structure and energetics. Lastly, based on the extent of QM overlaps and interaction energies, we propose geometric criteria using which these additional interactions can be efficiently tracked in broad database searches. 相似文献
14.
Multiple zigzag chains of length n and width m constitute an important class of regular graphene flakes of rectangular shape. The physical and chemical properties of these basic pericondensed benzenoids can be related to their various topological invariants, conveniently encoded as the coefficients of a combinatorial polynomial, usually referred to as the ZZ polynomial of multiple zigzag chains . The current study reports a novel method for determination of these ZZ polynomials based on a hypothesized extension to John–Sachs theorem, used previously to enumerate Kekulé structures of various benzenoid hydrocarbons. We show that the ZZ polynomial of the multiple zigzag chain can be conveniently expressed as a determinant of a Toeplitz (or almost Toeplitz) matrix of size consisting of simple hypergeometric polynomials. The presented analysis can be extended to generalized multiple zigzag chains , i.e., derivatives of with a single attached polyacene chain of length k. All presented formulas are accompanied by formal proofs. The developed theoretical machinery is applied for predicting aromaticity distribution patterns in large and infinite multiple zigzag chains and for computing the distribution of spin densities in biradical states of finite multiple zigzag chains . 相似文献
15.
Zahir Shah Rashid Jan Poom Kumam Wejdan Deebani Meshal Shutaywi 《Molecules (Basel, Switzerland)》2021,26(6)
Human immunodeficiency virus (HIV) is a life life-threatening and serious infection caused by a virus that attacks T-cells, which fight against infections and make a person susceptible to other diseases. It is a global public health problem with no cure; therefore, it is highly important to study and understand the intricate phenomena of HIV. In this article, we focus on the numerical study of the path-tracking damped oscillatory behavior of a model for the HIV infection of T-cells. We formulate fractional dynamics of HIV with a source term for the supply of new CD4+ T-cells depending on the viral load via the Caputo–Fabrizio derivative. In the formulation of fractional HIV dynamics, we replaced the constant source term for the supply of new T-cells from the thymus with a variable source term depending on the concentration of the viral load, and introduced a term that describes the incidence of the HIV infection of T-cells. We present a novel numerical scheme for fractional view analysis of the proposed model to highlight the solution pathway of HIV. We inspect the periodic and chaotic behavior of HIV for the given values of input factors using numerical simulations. 相似文献
16.
Danillo Valverde Adalberto V. S. de Araújo Antonio Carlos Borin 《Molecules (Basel, Switzerland)》2021,26(17)
The photophysical relaxation mechanisms of 1-cyclohexyluracil, in vacuum and water, were investigated by employing the Multi-State CASPT2 (MS-CASPT2, Multi-State Complete Active-Space Second-Order Perturbation Theory) quantum chemical method and Dunning’s cc-pVDZ basis sets. In both environments, our results suggest that the primary photophysical event is the population of the bright state. Afterwards, two likely deactivation pathways can take place, which is sustained by linear interpolation in internal coordinates defined via Z-Matrix scans connecting the most important characteristic points. The first one (Route 1) is the same relaxation mechanism observed for uracil, its canonical analogue, i.e., internal conversion to the ground state through an ethylenic-like conical intersection. The other route (Route 2) is the direct population transfer from the bright state to the triplet state via an intersystem crossing process involving the (/) singlet-triplet crossing point. As the spin-orbit coupling is not too large in either environment, we propose that most of the electronic population initially on the state returns to the ground following the same ultrafast deactivation mechanism observed in uracil (Route 1), while a smaller percentage goes to the triplet manifold. The presence of a minimum on the potential energy hypersurface in water can help to understand why experimentally it is noticed suppression of the triplet states population in polar protic solvent. 相似文献
17.
Steven van Terwingen Daniel Brüx Ruimin Wang Ulli Englert 《Molecules (Basel, Switzerland)》2021,26(13)
In the hydrochloride of a pyrazolyl-substituted acetylacetone, the chloride anion is hydrogen-bonded to the protonated pyrazolyl moiety. Equimolar co-crystallization with tetrafluorodiiodobenzene (TFDIB) leads to a supramolecular aggregate in which TFDIB is situated on a crystallographic center of inversion. The iodine atom in the asymmetric unit acts as halogen bond donor, and the chloride acceptor approaches the -hole of this TFDIB iodine subtending an almost linear halogen bond, with Cl···I = Å and Cl···I–C = 179.32(6)°. This contact is roughly orthogonal to the N–H···Cl hydrogen bond. An analysis of the electron density according to Bader’s Quantum Theory of Atoms in Molecules confirms bond critical points (bcps) for both short contacts, with = 0.129 for the halogen and e for the hydrogen bond. Our halogen-bonded adduct represents the prototype for a future class of co-crystals with tunable electron density distribution about the -hole contact. 相似文献
18.
19.
The changes in the local and global dynamics of azide-labelled lysozyme compared with that of the wild type protein are quantitatively assessed for all alanine residues along the polypeptide chain. Although attaching -N to alanine residues has been considered to be a minimally invasive change in the protein it is found that depending on the location of the alanine residue, the local and global changes in the dynamics differ. For Ala92, the change in the cross-correlated motions are minimal, whereas attaching -N to Ala90 leads to pronounced differences in the local and global correlations as quantified by the cross-correlation coefficients of the C atoms. We also demonstrate that the spectral region of the asymmetric azide stretch distinguishes between alanine attachment sites, whereas changes in the low frequency, far-infrared region are less characteristic. 相似文献
20.
Meei-Ju Yang Shwu-Yuan Lee Chieh-I Liu Shih-Hsuan Chen Iou-Zen Chen Tsung-Chen Su Jeu-Ming P. Yuann Chien-Wei Cheng Shiuh-Tsuen Huang Ji-Yuan Liang 《Molecules (Basel, Switzerland)》2020,25(24)
Tea is rich in catechins and aluminum. In this study, the process of catechin photolysis was applied as a model for examining the effects of aluminum chloride (AlCl3) on the structural changes of catechin and the alteration of aluminum complexes under blue light irradiation (BLI) at pH 8 using liquid chromatography and mass spectrometry techniques. Additionally, the effects of anions on catechin upon the addition of AlCl3 and treatment with BLI were also studied. In this study, when 1 mM catechin was treated with BLI, a superoxide anion radical () was generated in an air-saturated aqueous solution, in addition to forming a dimeric catechin (proanthocyanidin) via a photon-induced redox reaction. The relative percentage of catechin was found to be 59.0 and 95.7 for catechin treated with BLI and catechin upon the addition of 1 mM AlCl3 treated with BLI, respectively. It suggested that catechin treated with BLI could be suppressed by AlCl3, while AlCl3 did not form a complex with catechin in the photolytic system. However, under the same conditions, it was also found that the addition of AlCl3 inhibited the photolytic formation of and reduced the generation of proanthocyanidin, suggesting that the disconnection of proanthocyanidin was achieved by AlCl3 acting as a catalyst under treatment with BLI. The influence of 1 mM fluoride () and 1 mM oxalate () ions on the photolysis of 1 mM catechin upon the addition of 1 mM AlCl3 and treatment with BLI was found to be insignificant, implying that, during the photolysis of catechin, the Al species were either neutral or negatively charged and the aluminum species did not form a complex with anions in the photolytic system. Therefore, aluminum, which is an amphoteric species, has an inherent potential to stabilize the photolysis of catechin in an alkaline conditions, while suppressing the and proanthocyanidin generation via aluminum ion catalysis in the catechin/Al system under treatment with BLI. 相似文献