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41.
42.
Makowski M Sobolewski E Czaplewski C Ołdziej S Liwo A Scheraga HA 《The journal of physical chemistry. B》2008,112(36):11385-11395
The potentials of mean force of 21 heterodimers of the molecules modeling hydrophobic amino acid side chains: ethane (for alanine), propane (for proline), isobutane (for valine), isopentane (for leucine and isoleucine), ethylbenzene (for phenylalanine), methyl propyl sulfide (for methionine), and indole (for tryptophane) were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation. Analytical expressions consisting of the Gay-Berne term to represent effective van der Waals interactions and the cavity term proposed in our earlier work were fitted to the potentials of mean force. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules, are well represented by the analytical expressions for all systems; large deviations between the MD-determined PMF and the analytical approximations are observed for pairs involving the least spheroidal solutes: ethylbenzene, indole, and methyl propyl sulfide at short distances at which the PMF is high and, consequently, these regions are rarely visited. When data from the PMF within only 10 kcal/mol above the global minimum are considered, the standard deviation between the MD-determined and the fitted PMF is from 0.25 to 0.55 kcal/mol (the relative standard deviation being from 4% to 8%); it is larger for pairs involving nonspherical solute molecules. The free energies of contact computed from the PMF surfaces are well correlated with those determined from protein-crystal data with a slope close to that relating the free energies of transfer of amino acids (from water to n-octanol) to the average contact free energies determined from protein-crystal data. These observations justify future use of the determined potentials in coarse-grained protein-folding simulations. 相似文献
43.
Lapinski L Gerega A Sobolewski AL Nowak MJ 《The journal of physical chemistry. A》2008,112(2):238-248
Photochemical transformations of N-hydroxypyridine-2(1H)-thione and its deuterated isotopologue were studied using the matrix-isolation technique. Low-temperature Ar and N2 matrixes containing monomers of this compound were irradiated with continuous-wave near-UV light. Photogeneration of two products was observed in these experiments. The relative population of these photogenerated species was found to be dependent on the wavelength of the UV light used for irradiation. By comparison of the IR spectra of the photoproducts with the spectra simulated theoretically at the DFT(B3LYP)/6-311++G(d, p) level, the final and the intermediate products were identified as rotameric forms of 2-hydroxysulfanyl-pyridine. This is the first report on generation of this thioperoxy derivative of pyridine. The mechanism of photogeneration of 2-hydroxysulfanyl-pyridine involves a photoinduced cleavage of the N-O bond in N-hydroxypyridine-2(1H)-thione, generation of the .OH radical weakly bound with the remaining pyridylthiyl radical, and recombination of these two radicals by formation of the new -S-O- bond. A theoretical model supporting this interpretation was constructed on the basis of approximate coupled cluster (CC2) calculations of the potential energy surfaces of the ground and first excited singlet electronic states of the system. After electronic excitation of the monomeric N-hydroxypyridine-2(1H)-thione, the molecule evolves to the conical intersection with the potential energy surface of the ground state and then to the global minimum corresponding to 2-hydroxysulfanyl-pyridine. 相似文献
44.
Dr. Olaf W. Morawski Łukasz Kielesiński Prof. Daniel T. Gryko Prof. Andrzej L. Sobolewski 《Chemistry (Weinheim an der Bergstrasse, Germany)》2020,26(32):7281-7291
Linking a polarized coumarin unit with an aromatic substituent via an amide bridge results in weak electronic coupling that affects the intramolecular electron-transfer (ET) process. As a result of this, interesting solvent-dependent photophysical properties can be observed. In polar solvents, electron transfer in coumarin derivatives of this type induces a mutual twist of the electron-donating and -accepting molecular units (TICT process) that facilitates radiationless decay processes (internal conversion). In the dyad with the strongest intramolecular hydrogen bond, the planar form is stabilized, such that twisting can only occur in highly polar solvents, whereas a fast proton-coupled electron-transfer (PCET process) occurs in nonpolar n-alkanes. The kPCET rate constant decreases linearly with the energy of the fluorescence maximum in different solvents. This observation can be explained in terms of competition between electron- and proton-transfer from a highly polarized (ca. 15 D) and fluorescent locally excited (1LE) state to a much less polarized (ca. 4 D) charge-transfer (1CT) state, a unique occurrence. Photophysical measurements performed for a family of related coumarin dyads, together with results of quantum-chemical computations, give insight into the mechanism of the ET process, which is followed by either a TICT or a PCET process. Our results reveal that dielectric solvation of the excited state slows down the PCET process, even in nonpolar solvents. 相似文献
45.
Successive oxidation of transition metal(II) aqua complexes (M(II)OH(2) to M(III)OH) is a domain in which proton-coupled electron transfer reactions are extremely common. The mechanism of these PCET reactions-concerted or stepwise-is an important issue in the understanding and design of natural or artificial systems catalyzing the formation of dioxygen by four-electron oxidation of water. Concerted proton-coupled electron transfer from an aqua metal(II) to a hydroxo metal(III) complex requires the close proximity of a proton-accepting group with a pK value between those of the aqua complexes. Otherwise, stepwise electron-proton or proton-electron pathways involving high-energy intermediates are followed. Concerted proton-electron pathways involving water as proton-acceptor or proton-donor group are inefficient. Cyclic voltammetry of the title complex in buffered aqueous solution and re-examination of previous results for the same complex attached to an electrode surface are used to establish these conclusions, which provide a starting point on the route to higher degrees of oxidation, such as those involved in the catalysis of water oxidation. 相似文献
46.
Lapinski L Nowak MJ Sobolewski AL Kierdaszuk B 《The journal of physical chemistry. A》2006,110(15):5038-5046
A series of N4-hydroxycytosines, unsubstituted or substituted with methyl groups at N3 or C5 atoms of the heterocyclic ring, was studied using the matrix-isolation method. Depending on the absence or presence of the methyl substituent at N3 or C5 atoms (or at both of them) the syn or anti form of the compounds (or a mixture of both forms) was trapped from the gas phase into a low-temperature matrix. Upon UV (lambda > 295 nm) irradiation of the matrixes the syn --> anti as well as the anti --> syn photoisomerization reactions were observed. The syn and anti isomers of N4-hydroxycytosines were identified by comparing their experimental IR spectra with the theoretical spectra calculated at the DFT(B3LYP)/6-31G(d,p) level. For the majority of the studied compounds, the UV induced reactions led to a photostationary state. The position of the final photostationary state was found to be a sensitive function of weak interactions of a studied N4-hydroxycytosine with the matrix environment: solid argon or solid nitrogen. However, not all of the studied photoisomerizations led to a classical photostationary state. For some of the investigated N4-hydroxycytosines, the position of the photostationary state was shifted very strongly in favor of the photoproduct, whereas for some others the position was shifted so strongly in favor of the starting isomer that no photoisomerization was observed. These experimental findings were elucidated by theoretical investigations of the potential energy surfaces of the ground (S0) and first excited (S1) electronic states of N4-hydroxycytosine. The crucial result of these calculations (carried out at the CASSCF level) was the localization of a conical intersection between S0 and S1 at a structure with perpendicular orientation of the hydroxylimino group with respect to the heterocyclic ring. 相似文献
47.
Sobolewski E Makowski M Czaplewski C Liwo A Ołdziej S Scheraga HA 《The journal of physical chemistry. B》2007,111(36):10765-10774
The potentials of mean force (PMFs) were determined for systems involving formation of nonpolar dimers composed of methane, ethane, propane, isobutane, and neopentane, respectively, in water, using the TIP3P water model, and in vacuo. A series of umbrella-sampling molecular dynamics simulations with the AMBER force field was carried out for each pair in either water or in vacuo. The PMFs were calculated by using the weighted histogram analysis method (WHAM). The shape of the PMFs for dimers of all five nonpolar molecules is characteristic of hydrophobic interactions with contact and solvent-separated minima and desolvation maxima. The positions of all these minima and maxima change with the size of the nonpolar molecule, that is, for larger molecules they shift toward larger distances. The PMF of the neopentane dimer is similar to those of other small nonpolar molecules studied in this work, and hence the neopentane dimer is too small to be treated as a nanoscale hydrophobic object. The solvent contribution to the PMF was also computed by subtracting the PMF determined in vacuo from the PMF in explicit solvent. The molecular surface area model correctly describes the solvent contribution to the PMF together with the changes of the height and positions of the desolvation barrier for all dimers investigated. The water molecules in the first solvation sphere of the dimer are more ordered compared to bulk water, with their dipole moments pointing away from the surface of the dimer. The average number of hydrogen bonds per water molecule in this first hydration shell is smaller compared to that in bulk water, which can be explained by coordination of water molecules to the hydrocarbon surface. In the second hydration shell, the average number of hydrogen bonds is greater compared to bulk water, which can be explained by increased ordering of water from the first hydration shell; the net effect is more efficient hydrogen bonding between the water molecules in the first and second hydration shells. 相似文献
48.
为研究超高韧性水泥基复合材料(ultra-high toughness cementitious composites, UHTCC)在内埋炸药爆炸下的抗爆性能和损伤破坏规律,对不同炸药埋深下的UHTCC和高强混凝土(high-strength concrete, HSC)进行了内埋炸药抗爆实验。得到了两种材料靶体的破坏状态,并利用接触爆炸的实验结果计算出了两种材料的抗爆性能参数。结果表明,在相同条件下,UHTCC抗爆性能优于高强混凝土。为了进一步探究UHTCC的抗压强度、抗拉强度以及拉伸韧性对靶体在内埋炸药下抗爆性能的影响,首先,采用改进的K&C模型对炸药埋深为40 mm的超高韧性水泥基复合材料靶体进行数值模拟,模拟结果与实验结果基本吻合,并根据数值模拟的结果得到了爆炸冲击波沿靶体径向衰减速度大于轴向衰减速度这一规律,验证了数值模型的有效性;然后,通过调整改进K&C模型中与抗压强度、抗拉强度以及拉伸韧性相关的参数,数值预测了不同抗压强度、抗拉强度以及拉伸韧性下UHTCC靶体的破坏状态,发现增强UHTCC的韧性可以有效防止靶体发生整体性破坏,增大UHTCC的抗拉强度可以减小靶体迎爆面的开坑直径,增大UHTCC的抗压强度对减小开坑直径效果不明显。 相似文献
49.
Cihan Kürkçü Selgin AL Ziya Merdan Çağatay Yamçiçier Hülya Öztürk 《Chinese Journal of Physics (Taipei)》2018,56(3):783-792
The pressure induced phase transition of β-HgS is studied using an ab initio molecular dynamics simulation. The structural phase transformation from the zinc-blende structure to the NaCl-type structure (space group ) and from this structure to CsCl-type structure () with the application of hydrostatic pressure is predicted. Additionally, the electronic properties of HgS and various physical properties such as the lattice constants, the bulk modulus and the pressure derivative of the bulk modulus are revealed. Furthermore, these phase transitions are obtained using the total energy and enthalpy calculations. According to these calculations these transformations are occurring at about 20?GPa and 28?GPa for → and →, respectively. 相似文献
50.