显示样式:     当前期刊: The Journal of Chemical Physics    加入关注       排序: 导出
我的关注
我的收藏
您暂时未登录!
登录
  • Perspective: Multireference coupled cluster theories of dynamical electron correlation
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-17
    Francesco A. Evangelista

    Predicting the electronic structure and properties of molecular systems that display strong electron correlation effects continues to remain a fundamental theoretical challenge. This perspective discusses the recent progress and current challenges in multireference wave function methods for dynamical electron correlation, focusing on systematically improvable methods that go beyond the limitations of configuration interaction and perturbation theory.

    更新日期:2018-07-21
  • Communication: Fingerprints of reaction mechanisms in product distributions: Eley-Rideal-type reactions between D and CD3/Cu(111)
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-17
    Linsen Zhou, Bin Jiang, Maite Alducin, Hua Guo

    Through extensive direct dynamics studies of a prototypical Eley-Rideal type process, we demonstrate that fingerprints of microscopic reaction mechanisms can be identified in product distributions. Specifically, the umbrella vibration of CD4 formed by reacting gaseous D atoms with CD3 adsorbed on Cu(111) is highly excited if the reaction is initiated by a direct collision between the reactants due to the necessary inversion of the CD3 moiety. On the other hand, an indirect collision via a hot atom mechanism leads to much lower excitation in this product vibrational mode, and as such, an inversion is unnecessary. This fingerprint suggests an experimentally verifiable means to disentangle different mechanistic pathways.

    更新日期:2018-07-21
  • Communication: Heavy-Rydberg states of HD and the electron affinity of the deuterium atom
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-18
    Maximilian Beyer, Frédéric Merkt

    The electron affinity of the deuterium atom has been determined to be 6086.81(27) cm−1 from a measurement of the difference between the D+ + H− and H+ + D− ion-pair dissociation energies and a thermochemical cycle involving the electron affinity of H and the ionization energies of H and D. Heavy-Rydberg states and the ion-pair dissociation thresholds of HD were accessed with good efficiency using a three-photon excitation sequence through the B Σ u + 1 ( v = 22, N = 1) and H ¯   Σ g + 1 ( v = 9, N = 0) intermediate levels and the threshold positions were determined using the method of threshold-ion-pair-production spectroscopy.

    更新日期:2018-07-21
  • Communication: Computing the Helmholtz capacitance of charged insulator-electrolyte interfaces from the supercell polarization
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-19
    Chao Zhang

    Supercell modeling of an electrical double layer (EDL) at electrified solid-electrolyte interfaces is a challenge. The net polarization of EDLs arising from the fixed chemical composition setup leads to uncompensated EDLs under periodic boundary condition and convolutes the calculation of the Helmholtz capacitance [C. Zhang and M. Sprik, Phys. Rev. B 94, 245309 (2016)]. Here we provide a new formula based on the supercell polarization at zero electric field Ē = 0 (i.e., standard Ewald boundary condition) to calculate the Helmholtz capacitance of charged insulator-electrolyte interfaces and validate it using atomistic simulations. Results are shown to be independent of the supercell size. This formula gives a shortcut to compute the Helmholtz capacitance without locating the zero net charge state of EDL and applies directly to any standard molecular dynamics code where the electrostatic interactions are treated by the Ewald summation or its variants.

    更新日期:2018-07-21
  • Communication: Mode-dependent excited-state lifetime of phenol under the S1/S2 conical intersection
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-19
    Hsin Ying Lai, Wan Ru Jhang, Chien-Ming Tseng

    Phenol can serve as a model for examining the deactivation of the aromatic amino acid tyrosine following UV excitation, which mainly occurs through a repulsive πσ* state along the O–H bond. The reaction barrier formed by the conical intersection between the optically bright S1 (ππ*) state and the dissociative S2 (πσ*) state does not inhibit O–H bond rupture even though the excitation energy is below the barrier height. To examine the O–H bond-rupture dynamics in association with the initial excited vibrational modes, we used a picosecond laser to investigate the vibrational-mode-dependent excited-state lifetime of phenol under the S1/S2 conical intersection. Unexpectedly short lifetimes were observed in the S1 state for a″ symmetric vibrational modes (including v4, v16a, τOH, and v5). These results clarify recent theoretical calculations showing that the relaxation from S1 to S2 either occurs via symmetry-allowed non-adiabatic transitions or is topographically linked to a lower energy minimum on the multidimensional potential energy surface.

    更新日期:2018-07-21
  • Communication: Infrared photodissociation spectroscopy of the H6+ cation in the gas phase
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-20
    David C. McDonaldII, J. Philipp Wagner, Michael A. Duncan

    The H6+ cation was generated in a pulsed-discharge supersonic expansion of hydrogen and mass-selected in a time-of-flight spectrometer. Its vibrational spectrum was measured in the region of 2050–4550 cm−1 using infrared photodissociation with a tunable OPO/OPA laser system. The H6+ photodissociates, producing H5+, H4+, and H3+ fragments; each of these fragment channels has a different spectrum. Computational studies identify two low-lying isomers described in previous work, whose energies were evaluated at the CCSD(T)/cc-pVTZ//MP2/cc-pVTZ level of theory. A D2d species having an H2+ cation bridging between two perpendicular H2 molecules is the global minimum structure. A Cs structure with an H3+ core ion bound to both H2 and an H atom lies 4.0 kcal mol−1 higher in energy. Anharmonic vibrational spectra were computed for each of these isomers with second-order vibrational perturbation theory (VPT2) in combination with density functional theory at the B2PLYP/cc-pVTZ level. The comparison between experimental and predicted spectra confirms the presence of both the D2d and Cs structures and explains the spectra in different fragmentation channels. Although we find reasonable agreement between the experiment and the spectra predicted by VPT2 computations, a more sophisticated computational approach is needed to better understand this complex system.

    更新日期:2018-07-21
  • DeePCG: Constructing coarse-grained models via deep neural networks
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-16
    Linfeng Zhang, Jiequn Han, Han Wang, Roberto Car, Weinan E

    We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called the Deep Coarse-Grained Potential (abbreviated DeePCG), exploits a carefully crafted neural network to construct a many-body coarse-grained potential. The network is trained with full atomistic data in a way that preserves the natural symmetries of the system. The resulting model is very accurate and can be used to sample the configurations of the coarse-grained variables in a much faster way than with the original atomistic model. As an application, we consider liquid water and use the oxygen coordinates as the coarse-grained variables, starting from a full atomistic simulation of this system at the ab initio molecular dynamics level. We find that the two-body, three-body, and higher-order oxygen correlation functions produced by the coarse-grained and full atomistic models agree very well with each other, illustrating the effectiveness of the DeePCG model on a rather challenging task.

    更新日期:2018-07-21
  • Post-CCSD(T) contributions to total atomization energies in multireference systems
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-16
    Amir Karton

    We examine the magnitude and the basis set convergence of post-coupled-cluster with single, double, and perturbative triple excitations (CCSD(T)) contributions (up to CCSDTQ567) for a wide and diverse set of 21 first- and second-row molecules with up to four non-hydrogen atoms. We focus on multireference systems for which post-CCSD(T) effects are particularly pronounced. The considered molecules are BN(1∑+), C2(1∑+), O2, FO, P2, S2, ClO, N2O, NO2, O3, FNO, FO2, F2O, S2O, S3, ClNO, ClOO, Cl2O, N2C2, P4, and S4. This set spans the gamut from molecules dominated by moderate nondynamical correlation (e.g., FO, ClO, NO2, S2O, N2C2, and P4) to systems dominated by strong nondynamical correlation (e.g., BN, C2, FO2, O3, ClOO, and S4). We examine the basis set convergence of the CCSDT, CCSDT(Q), CCSDTQ, CCSDTQ(5), CCSDTQ5, CCSDTQ5(6), CCSDTQ56, CCSDTQ56(7), and CCSDTQ567 methods. The largest basis sets employed in each category are cc-pV6Z (CCSDT(Q)), cc-pV5Z (CCSDTQ), cc-pVTZ (CCSDTQ5(6)), and cc-pVDZ (CCSDTQ567). Apart from examining the basis-set convergence of post-CCSD(T) contributions near the one-particle basis-set limit, this work explores cost-effective approaches for obtaining these contributions from fairly small basis sets. We consider both effective basis-set extrapolations and scaling factors. An important finding is that extrapolating the perturbative connected quadruples, (Q), from the cc-pVDZ(4s3p1d) and cc-pVTZ basis sets yields near basis-set limit results and represents a significant improvement relative to cc-pV{D,T}Z extrapolation at no additional computational cost (where cc-pVDZ(4s3p1d) is an extended version of the cc-pVDZ basis set). Combining the (Q)/cc-pV{D(4s3p1d),T}Z extrapolations with the fully iterative connected quadruples, Q–(Q), contribution calculated with the cc-pVDZ (or even the cc-pVDZ(3s2p)) basis set is a cost-effective way for obtaining the connected quadruples component close to the basis-set limit (where cc-pVDZ(3s2p) is a truncated version of the cc-pVDZ basis set). In addition, we show that the (5)/cc-pVDZ(3s2p) and (6)/cc-pVDZ(3s2p) components provide reasonable approximations for the connected quintuple and sextuple components close to the basis-set limit, respectively.

    更新日期:2018-07-21
  • On the low magnetic field effect in radical pair reactions
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-17
    Alan M. Lewis, Thomas P. Fay, David E. Manolopoulos, Christian Kerpal, Sabine Richert, Christiane R. Timmel

    Radical pair recombination reactions are known to be sensitive to the application of both low and high magnetic fields. The application of a weak magnetic field reduces the singlet yield of a singlet-born radical pair, whereas the application of a strong magnetic field increases the singlet yield. The high field effect arises from energy conservation: when the magnetic field is stronger than the sum of the hyperfine fields in the two radicals, S → T± transitions become energetically forbidden, thereby reducing the number of pathways for singlet to triplet interconversion. The low field effect arises from symmetry breaking: the application of a weak magnetic field lifts degeneracies among the zero field eigenstates and increases the number of pathways for singlet to triplet interconversion. However, the details of this effect are more subtle and have not previously been properly explained. Here we present a complete analysis of the low field effect in a radical pair containing a single proton and in a radical pair in which one of the radicals contains a large number of hyperfine-coupled nuclear spins. We find that the new transitions that occur when the field is switched on are between S and T0 in both cases, and not between S and T± as has previously been claimed. We then illustrate this result by using it in conjunction with semiclassical spin dynamics simulations to account for the observation of a biphasic-triphasic-biphasic transition with increasing magnetic field strength in the magnetic field effect on the time-dependent survival probability of a photoexcited carotenoid-porphyrin-fullerene radical pair.

    更新日期:2018-07-21
  • Accurate spin-densities based on the domain-based local pair-natural orbital coupled-cluster theory
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-19
    Masaaki Saitow, Frank Neese

    Exploiting locality in the electron correlation reduces the computational cost for solving the Coupled-Cluster (CC) equations. This is important for making CC theory applicable to routine computational chemistry applications where it promises to deliver results of “gold-standard” quality. Recently, we have proposed a series of CC formulations in the domain-based local pair-natural orbital framework [DLPNO-coupled-cluster with singles and doubles (CCSD) and DLPNO-coupled-cluster singles and doubles with perturbative triples] which are designed to reproduce approximately 99.9% of the canonical correlation energy. In our previous work, the DLPNO-CCSD method has been extended to the high-spin open-shell reference and shown to possess comparable accuracy to the closed-shell counterpart [M. Saitow et al., J. Chem. Phys. 146, 164105 (2017)]. The so-called Λ-equations have been formulated in the DLPNO framework for the closed-shell species as an exact derivative of the DLPNO-CCSD Lagrangian with respect to the PNO-based cluster amplitudes [D. Datta et al., J. Chem. Phys. 145, 114101 (2016)]. In this paper, we extend the DLPNO-based Lagrangian scheme to the high-spin open-shell reference cases, thus enabling the accurate computation of the electron- and spin-densities for large open-shell species. We apply this newly developed approach to various first-order electronic and magnetic properties such as isotropic and anisotropic components in the hyperfine coupling interactions and the electric field gradient. We demonstrate that the DLPNO-CCSD results converge toward the respective canonical CC density and also that the DLPNO-CCSD-based properties are more accurate than the conventional density functional theory (DFT) results in real-life applications. The additional computational cost is not more than one energy evaluation in the DLPNO-CCSD framework.

    更新日期:2018-07-21
  • Locally coupled open subsystems: A formalism for affordable electronic structure calculations featuring fractional charges and size consistency
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-19
    Martín A. Mosquera, Mark A. Ratner, George C. Schatz

    This manuscript introduces a methodology (within the Born-Oppenheimer picture) to compute electronic ground-state properties of molecules and solids/surfaces with fractionally occupied components. Given a user-defined division of the molecule into subsystems, our theory uses an auxiliary global Hamiltonian that is defined as the sum of subsystem Hamiltonians, plus the spatial integral of a second-quantized local operator that allows the electrons to be transferred between subsystems. This electron transfer operator depends on a local potential that can be determined using density functional approximations and/or other techniques such as machine learning. The present framework employs superpositions of tensor-product wave functions, which can satisfy size consistency and avoid spurious fractional charges at large bond distances. The electronic population of each subsystem is in general a positive real number and is obtained from wave-function amplitudes, which are calculated by means of ground-state matrix diagonalization (or matrix propagation in the time-dependent case). Our method can provide pathways to explore charge-transfer effects in environments where dividing the molecule into subsystems is convenient and to develop computationally affordable electronic structure algorithms.

    更新日期:2018-07-21
  • Quasiparticle energy spectra of isolated atoms from coupled-cluster singles and doubles (CCSD): Comparison with exact CI calculations
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-19
    Hirofumi Nishi, Taichi Kosugi, Yoritaka Furukawa, Yu-ichiro Matsushita

    In this study, we have calculated single-electron energy spectra via the Green’s function based on the coupled-cluster singles and doubles (GFCCSD) method for isolated atoms from H to Ne. In order to check the accuracy of the GFCCSD method, we compared the results with the exact ones calculated from the full-configuration interaction. Consequently, we have found that the GFCCSD method reproduces not only the correct quasiparticle peaks but also satellite ones by comparing the exact spectra with the 6-31G basis set. It is also found that open-shell atoms such as C atom exhibit Mott gaps at the Fermi level, which the exact density-functional theory fails to describe. The GFCCSD successfully reproduces the Mott highest-occupied molecular orbital and lowest-unoccupied molecular orbital gaps even quantitatively. We also discussed the origin of satellite peaks as shake-up effects by checking the components of wave function of the satellite peaks. The GFCCSD is a novel cutting edge to investigate the electronic states in detail.

    更新日期:2018-07-21
  • Learning dynamic Boltzmann distributions as reduced models of spatial chemical kinetics
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-20
    Oliver K. Ernst, Thomas Bartol, Terrence Sejnowski, Eric Mjolsness

    Finding reduced models of spatially distributed chemical reaction networks requires an estimation of which effective dynamics are relevant. We propose a machine learning approach to this coarse graining problem, where a maximum entropy approximation is constructed that evolves slowly in time. The dynamical model governing the approximation is expressed as a functional, allowing a general treatment of spatial interactions. In contrast to typical machine learning approaches which estimate the interaction parameters of a graphical model, we derive Boltzmann-machine like learning algorithms to estimate directly the functionals dictating the time evolution of these parameters. By incorporating analytic solutions from simple reaction motifs, an efficient simulation method is demonstrated for systems ranging from toy problems to basic biologically relevant networks. The broadly applicable nature of our approach to learning spatial dynamics suggests promising applications to multiscale methods for spatial networks, as well as to further problems in machine learning.

    更新日期:2018-07-21
  • Excitation energies from diffusion Monte Carlo using selected configuration interaction nodes
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-20
    Anthony Scemama, Anouar Benali, Denis Jacquemin, Michel Caffarel, Pierre-François Loos

    Quantum Monte Carlo (QMC) is a stochastic method that has been particularly successful for ground-state electronic structure calculations but mostly unexplored for the computation of excited-state energies. Here, we show that within a Jastrow-free QMC protocol relying on a deterministic and systematic construction of nodal surfaces using selected configuration interaction (sCI) expansions, one is able to obtain accurate excitation energies at the fixed-node diffusion Monte Carlo (FN-DMC) level. This evidences that the fixed-node errors in the ground and excited states obtained with sCI wave functions cancel out to a large extent. Our procedure is tested on two small organic molecules (water and formaldehyde) for which we report all-electron FN-DMC calculations. For both the singlet and triplet manifolds, accurate vertical excitation energies are obtained with relatively compact multideterminant expansions built with small (typically double-ζ) basis sets.

    更新日期:2018-07-21
  • Potential of mean force for two nanocrystals: Core geometry and size, hydrocarbon unsaturation, and universality with respect to the force field
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-20
    Curt Waltmann, Nathan Horst, Alex Travesset

    We present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We analyze large cores (up to 10 nm in diameter) and ligands with unsaturated carbon bonds (oleic acid) and we investigate the accuracy of the computed potential of mean force by comparing different force fields. We also analyze the vortices that determine the bonding, including the case of asymmetric nanocrystals, and discuss effects related to the intrinsic anisotropy of the core. Overall our results are in agreement with the predictions of the recently proposed orbifold topological model.

    更新日期:2018-07-21
  • Optimal control RF pulses for excitation and suppression of NMR signals in a conductive medium
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-20
    Boris Kharkov, Leonard Strouk, Thomas E. Skinner, Alexej Jerschow

    In this work, optimal control theory was used to design efficient excitation schemes in highly conductive materials, where both the radio frequency field strength and phase vary as a function of penetration depth. A pulse was designed to achieve phase alignment between signals at different depths within the conductor and thus to obtain higher signals from that region. In addition, an efficient suppression pulse was designed by insuring mutual suppression between the signals from various depths in the sample. The performance of the new approach was demonstrated experimentally for a bulk lithium sample for the excitation problem and for a biphasic metal/liquid sample for the selective suppression pulse.

    更新日期:2018-07-21
  • Ultraviolet relaxation dynamics in uracil: Time-resolved photoion yield studies using a laser-based thermal desorption source
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-17
    Omair Ghafur, Stuart W. Crane, Michal Ryszka, Jana Bockova, Andre Rebelo, Lisa Saalbach, Simone De Camillis, Jason B. Greenwood, Samuel Eden, Dave Townsend

    Wavelength-dependent measurements of the RNA base uracil, undertaken with nanosecond ultraviolet laser pulses, have previously identified a fragment at m/z = 84 (corresponding to the C3H4N2O+ ion) at excitation wavelengths ≤232 nm. This has been interpreted as a possible signature of a theoretically predicted ultrafast ring-opening occurring on a neutral excited state potential energy surface. To further investigate the dynamics of this mechanism, and also the non-adiabatic dynamics operating more generally in uracil, we have used a newly built ultra-high vacuum spectrometer incorporating a laser-based thermal desorption source to perform time-resolved ion-yield measurements at pump wavelengths of 267 nm, 220 nm, and 200 nm. We also report complementary data obtained for the related species 2-thiouracil following 267 nm excitation. Where direct comparisons can be made (267 nm), our findings are in good agreement with the previously reported measurements conducted on these systems using cold molecular beams, demonstrating that the role of initial internal energy on the excited state dynamics is negligible. Our 220 nm and 200 nm data also represent the first reported ultrafast study of uracil at pump wavelengths <250 nm, revealing extremely rapid (<200 fs) relaxation of the bright S3(1ππ*) state. These measurements do not, however, provide any evidence for the appearance of the m/z = 84 fragment within the first few hundred picoseconds following excitation. This key finding indicates that the detection of this specific species in previous nanosecond work is not directly related to an ultrafast ring-opening process. An alternative excited state process, operating on a more extended time scale, remains an open possibility.

    更新日期:2018-07-21
  • Quantum dynamics calculations reveal temperature independence of kinetic isotope effect of the OH + HBr/DBr reaction
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-16
    Yuping Wang, Dunyou Wang

    The reaction of OH radicals with HBr plays a key role in atmospheric chemistry as the reaction, OH + HBr → Br + H2O, produces Br atoms that destroy ozone. The experimental measurements of the kinetic isotope effect of k(OH + HBr)/k(OH + DBr) found that the kinetic isotope effects are temperature-independent. However, previous quasi-classical trajectory calculations on an accurate ab initio potential energy surface showed that the kinetic isotope effect is temperature-dependent. By contrast, the present full-dimensional time-dependent quantum dynamics calculations on the same potential energy surface find that the kinetic isotope effect is temperature-independent, agreeing well with the experimental studies both qualitatively and quantitatively. Furthermore, the rate constants from both quantum dynamics and quasi-classical trajectory calculations have a peak at around 15 K whereas the experimental data are not available in this low temperature range. The good agreement of the temperature-dependence of kinetic isotope effects between the present quantum dynamics calculations and the experimental measurements indicates that the kinetic isotope effect of k(OH + HBr)/k(OH + DBr) should be temperature-independent and the peak of the rate constants from the theoretical calculations call for experimental measurements at a very low temperature range.

    更新日期:2018-07-21
  • Spectroscopy and formation of lanthanum-hydrocarbon radicals formed by C—H and C—C bond activation of 1-pentene and 2-pentene
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-16
    Wenjin Cao, Yuchen Zhang, Silver Nyambo, Dong-Sheng Yang

    La atom reactions with 1-pentene and 2-pentene are carried out in a laser-vaporization molecular beam source. The two reactions yield the same metal-hydrocarbon products from the dehydrogenation and carbon–carbon bond cleavage of the pentene molecules. The dehydrogenated species La(C5H8) is the major product, whereas the carbon–carbon bond cleaved species La(C2H2) and La(C3H4) are the minor ones. La(C10H18) is also observed and is presumably formed by La(C5H8) addition to a second pentene molecule. La(C5H8) and La(C2H2) are characterized with mass-analyzed threshold ionization (MATI) spectroscopy and quantum chemical computations. The MATI spectra of each species from the two reactions exhibit the same transitions. Adiabatic ionization energies and metal-ligand stretching frequencies are determined for the two species, and additional methyl bending and torsional frequencies are measured for the larger one. Five possible isomers are considered for La(C5H8), and a C1 metallacyclopentene (Iso A) is identified as the most possible isomer. La(C2H2) is confirmed to be a C2v metallacyclopropene. The ground electronic state of each species is a doublet with a La 6s1-based electron configuration, and ionization yields a singlet state. The formation of the lanthanacyclopentene includes La addition to the C=C double bond, La insertion into two C(sp3)—H bonds, and concerted dehydrogenation. For the 2-pentene reaction, the formation of the five-membered ring may also involve 2-pentene to 1-pentene isomerization. In addition to the metal addition and insertion, the formation of the three-membered metallacycle from 1-pentene includes C(sp3)—C(sp3) bond breakage and hydrogen migration from La to C(sp3), whereas its formation from 2-pentene may involve the ligand isomerization.

    更新日期:2018-07-21
  • Cross sections for electron scattering from thiophene for a broad energy range
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-16
    Alexandra Loupas, Ana. I. Lozano, Francisco Blanco, Jimena D. Gorfinkiel, Gustavo García

    We present cross sections for elastic and inelastic electron scattering from thiophene calculated in the energy range 0.1-1000 eV. The R-matrix and independent atom representation-screening-corrected additivity rule (IAM-SCAR) methods were used for low-energy and intermediate and high scattering energies, respectively. The results provide a consistent picture of the scattering process in the whole energy range. The effect of including an interference term in the IAM-SCAR approach is considered. Agreement with prior theoretical results is also discussed.

    更新日期:2018-07-21
  • The photoelectron spectra of the isomeric 1- and 2-methyltetrazoles; their equilibrium structures and vibrational analysis by ab initio calculations
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-17
    Michael H. Palmer, Marcello Coreno, Monica de Simone, Cesare Grazioli, Søren Vrønning Hoffmann, Nykola C. Jones, Kirk A. Peterson, R. Alan Aitken, Cécile Rouxel

    New synchrotron based studies of the photoelectron ionization spectra (PES) for the isomeric 1- and 2-methyltetrazoles (1- and 2-MeTet) show markedly higher resolution than previous reports. The unusual spectral profiles suggest that a considerable overlay of the ionic states occurs for both molecules. Under these circumstances of near degeneracy of two or more ionic states, mutual annihilation of vibrational fine structure occurs for all except the strongest vibrational states; the PES just reflects the resultants rather than full spectra. Theoretical determination of the adiabatic ionization energies (AIEs) proved a challenge; the most successful method was second order Møller-Plesset perturbation theory (MP2). These calculations suggest that the lowest PES bands for both isomers contain ionization both from lone pair σ-orbitals (2A′) on the N-atoms (LPN) and π-orbitals (2A″). The lowest experimental AIEs are as follows: 1-MeTet is 10.315 eV assigned to 12A′, while 2-MeTet is 10.543 eV assigned to 12A″. Franck-Condon analysis shows that the lowest ionization energy regions of both spectra are dominated by IE from the LPN 2A′ manifold, even though the 2A″ states have a higher absolute intensity. In this example, we have utilized a VUV Rydberg state to assist simplification of the PES; more frequently, the PES assignment is simpler and assists the location of Rydberg states in the VUV. The very slow spectral onset for 2-MeTet demonstrates the importance of vertical ionization energy calculations since maxima are more readily measured than slow onsets. These were performed at the equilibrium structure of the X1A′ state, using both multi-reference multi-root configuration interaction and the ionization potential variant of the equations-of-motion coupled cluster method, with single and double excitations (EOMIP-CCSD). This enabled the principal ionization bands to be identified over a wider range of energy. Attempts to study the higher ionic states by EOMIP-CCSD showed that several states of each symmetry are close to degenerate for 1-MeTet, in particular. A multi-configuration self-consistent field study confirmed the small separation of ionic states, but state switching during the optimization process largely disabled this method.

    更新日期:2018-07-21
  • Intermolecular dissociation energies of 1-naphthol·n-alkane complexes
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-17
    Richard Knochenmuss, Surajit Maity, Franziska Balmer, Charlotte Müller, Samuel Leutwyler

    Using the stimulated-emission-pumping/resonant 2-photon ionization (SEP-R2PI) method, we have determined accurate intermolecular dissociation energies D0 of supersonic jet-cooled intermolecular complexes of 1-naphthol (1NpOH) with alkanes, 1NpOH·S, with S = methane, ethane, propane, and n-butane. Experimentally, the smaller alkanes form a single minimum-energy structure, while 1-naphthol·n-butane forms three different isomers. The ground-state dissociation energies D0(S0) for the complexes with propane and n-butane (isomers A and B) were bracketed within ±0.5%, being 16.71 ± 0.08 kJ/mol for S = propane and 20.5 ± 0.1 kJ/mol for isomer A and 20.2 ± 0.1 kJ/mol for isomer B of n-butane. All 1NpOH·S complexes measured previously exhibit a clear dissociation threshold in their hot-band detected SEP-R2PI spectra, but weak SEP-R2PI bands are observed above the putative dissociation onset for the methane and ethane complexes. We attribute these bands to long-lived complexes that retain energy in rotation-type intermolecular vibrations, which couple only weakly to the dissociation coordinates. Accounting for this, we find dissociation energies of D0(S0) = 7.98 ± 0.55 kJ/mol (±7%) for S = methane and 14.5 ± 0.28 kJ/mol (±2%) for S = ethane. The D0 values increase by only 1% upon S0 → S1 excitation of 1-naphthol. The dispersion-corrected density functional theory methods B97-D3, B3LYP-D3, and ωB97X-D predict that the n-alkanes bind dispersively to the naphthalene “Face.” The assignment of the complexes to Face structures is supported by the small spectral shifts of the S0 → S1 electronic origins, which range from +0.5 to −15 cm−1. Agreement with the calculated dissociation energies D0(S0) is quite uneven, the B97-D3 values agree within 5% for propane and n-butane, but differ by up to 20% for methane and ethane. The ωB97X-D method shows good agreement for methane and ethane but overestimates the D0(S0) values for the larger n-alkanes by up to 20%. The agreement of the B3LYP-D3 D0 values is intermediate between the other two methods.

    更新日期:2018-07-21
  • Ab initio calculation of femtosecond-time-resolved photoelectron spectra of NO2 after excitation to the A-band
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-17
    Andres Tehlar, Aaron von Conta, Yasuki Arasaki, Kazuo Takatsuka, Hans Jakob Wörner

    We present calculations of time-dependent photoelectron spectra of NO2 after excitation to the A-band for comparison with extreme-ultraviolet (XUV) time-resolved photoelectron spectroscopy. We employ newly calculated potential energy surfaces of the two lowest-lying coupled 2A′ states obtained from multi-reference configuration-interaction calculations to propagate the photo-excited wave packet using a split-step-operator method. The propagation includes the nonadiabatic coupling of the potential surfaces as well as the explicit interaction with the pump pulse centered at 3.1 eV (400 nm). A semiclassical approach to calculate the time-dependent photoelectron spectrum arising from the ionization to the eight energetically lowest-lying states of the cation allows us to reproduce the static experimental spectrum up to a binding energy of 16 eV and enables direct comparisons with XUV time-resolved photoelectron spectroscopy.

    更新日期:2018-07-21
  • Normal and resonant Auger spectroscopy of isocyanic acid, HNCO
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-19
    F. Holzmeier, T. J. A. Wolf, C. Gienger, I. Wagner, J. Bozek, S. Nandi, C. Nicolas, I. Fischer, M. Gühr, R. F. Fink

    In this paper, we investigate HNCO by resonant and nonresonant Auger electron spectroscopy at the K-edges of carbon, nitrogen, and oxygen, employing soft X-ray synchrotron radiation. In comparison with the isosteric but linear CO2 molecule, spectra of the bent HNCO molecule are similar but more complex due to its reduced symmetry, wherein the degeneracy of the π-orbitals is lifted. Resonant Auger electron spectra are presented at different photon energies over the first core-excited 1s → 10a′ resonance. All Auger electron spectra are assigned based on ab initio configuration interaction computations combined with the one-center approximation for Auger intensities and moment theory to consider vibrational motion. The calculated spectra were scaled by a newly introduced energy scaling factor, and generally, good agreement is found between experiment and theory for normal as well as resonant Auger electron spectra. A comparison of resonant Auger spectra with nonresonant Auger structures shows a slight broadening as well as a shift of the former spectra between −8 and −9 eV due to the spectating electron. Since HNCO is a small molecule and contains the four most abundant atoms of organic molecules, the reported Auger electron decay spectra will provide a benchmark for further theoretical approaches in the computation of core electron spectra.

    更新日期:2018-07-21
  • The photoinduced isomerization mechanism of the 2-(1-(methylimino)methyl)-6-chlorophenol (SMAC): Nonadiabatic surface hopping dynamics simulations
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-20
    Li Zhao, Jianyong Liu, Panwang Zhou

    The photophysical properties of the Schiff base family are crucial for their applications such as molecular switches and molecular memories. However, it was found that the photophysical behavior is not uniform for all Schiff base molecules, which shows a significant substituent dependent property. In this article, we studied the photoisomerization mechanism of one Schiff base chlorosubstituted derivative 2-(1-(methylimino)methyl)-6-chlorophenol by employing geometrical optimization, energy profiles scanning, and on-the-fly dynamical simulations. Three types of minimum energy conical intersections were located on the S1/S0 crossing seam, with two characterized by twisting motion of the C=N bond and one featured with the excited state intramolecular proton transfer process and then twisting motion around the C=C bond [excited-state intramolecular proton transfer process (ESIPT)-then-twisting]. By a combination of the dynamics simulation results with the energy profiles scanned along with the ESIPT coordinate, it was found that the photophysical property of the targeted molecule is different from that of most Schiff base members, which prefer to decay by a twisting motion around the C=N bridge bond rather than the ESIPT-then-twisting channel. The minor ESIPT channel is probably governed by a tunneling mechanism. The proposed deactivation mechanism can provide a reasonable explanation for the observations in the experiment and would provide fundamental indications for further design of new and efficient photochromic products.

    更新日期:2018-07-21
  • Effects of pressure on the structure and lattice dynamics of ammonium perchlorate: A combined experimental and theoretical study
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-18
    Matthew P. Kroonblawd, Batikan Koroglu, Joseph M. Zaug, Philip F. Pagoria, Nir Goldman, Eran Greenberg, Vitali B. Prakapenka, Martin Kunz, Sorin Bastea, Elissaios Stavrou

    Ammonium perchlorate NH4ClO4 (AP) was studied using synchrotron angle-dispersive X-ray powder diffraction (XRPD) and Raman spectroscopy. A diamond-anvil cell was used to compress AP up to 50 GPa at room temperature (RT). Density functional theory (DFT) calculations were performed to provide further insight and comparison to the experimental data. A high-pressure barite-type structure (Phase II) forms at ≈4 GPa and appears stable up to 40 GPa. Refined atomic coordinates for Phase II are provided, and details for the Phase I → II transition mechanics are outlined. Pressure-dependent enthalpies computed for DFT-optimized crystal structures confirm the Phase I → II transition sequence, and the interpolated transition pressure is in excellent agreement with the experiment. Evidence for additional (underlying) structural modifications include a marked decrease in the Phase II b′-axis compressibility starting at 15 GPa and an unambiguous stress relaxation in the normalized stress-strain response at 36 GPa. Above 47 GPa, XRD Bragg peaks begin to decrease in amplitude and broaden. The apparent loss of crystalline long-range order likely signals the onset of amorphization. Three isostructural modifications were discovered within Phase II via Raman spectroscopy. A revised RT isothermal phase diagram is discussed based on the findings of this study.

    更新日期:2018-07-21
  • Composition effect on thermophobicity of ternary mixtures: An enhanced molecular dynamics method
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-18
    Sylvie Antoun, M. Ziad Saghir, S. Srinivasan

    Thermodiffusion or the Ludwig-Soret effect is known as the cross effect between the temperature gradient and induced separation of mixture species in multicomponent mixtures. The performance of the boundary driven non-equilibrium molecular dynamics enhanced heat exchange (eHEX) algorithm was validated by evaluating the sign and magnitude of the thermodiffusion process in methane/n-butane/n-dodecane (nC1–nC4–nC12) ternary mixtures. The eHEX algorithm consists of an extended version of the HEX algorithm with an improved energy conservation property. In addition to this, the transferable potentials for phase equilibria-united atom augmented force field was employed in all molecular dynamics (MD) simulations to accurately represent molecular interactions in the fluid. Our newly employed MD algorithm was capable to appropriately reflect the thermophobicity concept and the coupled effect of relative density and mole fraction of the mixture species on the thermodiffusion process. The separation ratio of the ternary mixture for five different compositions (at 333.15 K and 35 MPa) showed good agreement with experimental data and better accuracy in predicting the sign change of the intermediate component (nC4) as its concentration in the mixture increases, when compared to other MD models.

    更新日期:2018-07-21
  • Transient structured fluctuations in a two-dimensional system with multiple ordered phases
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-19
    Zach Krebs, Ari B. Roitman, Linsey M. Nowack, Chris Liepold, Binhua Lin, Stuart A. Rice

    We report the structure of transient fluctuations in the liquid phase of a two-dimensional system that exhibits several ordered phases with different symmetries. The density-temperature phase diagram of the system studied, composed of particles with a repulsive shouldered soft-core pair interaction, has regions with stable liquid and hexatic phases, a square solid phase, two separate hexagonal solid phases, and a quasi-crystalline phase with 12-fold symmetry. We have examined the character of the structured fluctuations by computing the same-time aperture cross correlation function of particle configurations in several fluid regions near to and far from phase transition lines. The two primary goals of our study are (1) determination if the spectrum of structures of the fluctuations in the liquid is broader than or limited to the motifs exhibited by the ordered phases supported by the system and (2) determination of the density domains in the liquid that support particular transient structured fluctuations. In the system studied, along a low-temperature isotherm in the temperature-density plane that intersects all the ordered phases we find that the liquid phase exhibits structured fluctuations with hexagonal symmetry near both liquid-hexatic transition lines. Along the same isotherm and in the stable liquid between the lower density hexatic-to-liquid and the higher density liquid-to-square solid transitions, we find that transient hexagonal ordered fluctuations dominate the liquid region near the hexatic-to-liquid transition and square ordered fluctuations dominate the liquid region near the liquid-to square solid transition, but both of these structured fluctuations occur at all densities between these transition lines. At a higher temperature, at phase points in the liquid above, but close to the density maximum of an underlying transition, there are ordered fluctuations that can be correlated with the structure of the lower temperature phase. Although it is expected that very close to a liquid-ordered phase boundary a structured fluctuation in the liquid will have the same symmetry as the ordered phase, it is not obvious that structured fluctuations in thermodynamic states deep in the liquid phase will be similarly restricted. The most striking result of our calculations is that no evidence is found in the liquid phase for structured fluctuations with other symmetries than those of the ordered phases of the system.

    更新日期:2018-07-21
  • Nonlinear optical response of a gold surface in the visible range: A study by two-color sum-frequency generation spectroscopy. II. Model for metal nonlinear susceptibility
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-17
    B. Busson, L. Dalstein

    We present a modeling of the nonlinear optical response of a metal surface in order to account for recent experimental results from two-color Sum-Frequency Generation (SFG) experiments on gold. The model allows calculating the surface and bulk contributions and explicitly separates free and bound electron terms. Contrary to the other contributions, the perpendicular surface component is strongly model-dependent through the surface electron density profiles. We consider three electron density schemes at the surface, with free and bound electrons overlapping or spilling out of the bulk, for its calculation. The calculated SFG signals from the metal rely only on bulk quantities and do not need an explicit definition of the density profiles. In the particular case of gold, when the free electrons overlap with the bound ones or spill out of the bulk, the free electron response completely dominates through the perpendicular surface terms. When the bound electrons spill out, the situation is more balanced, still in favor of the free electrons, with lower amplitudes and different dispersion line shapes. As for silver, the free electron contributions dominate and the calculated slow amplitude growth from blue to red follows the experimental trends.

    更新日期:2018-07-21
  • From C60 “trilliumons” to “trilliumenes:” Self-assembly of 2D fullerene nanostructures on metal-covered silicon and germanium
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-17
    A. V. Zotov, D. A. Olyanich, V. V. Mararov, T. V. Utas, L. V. Bondarenko, A. Y. Tupchaya, D. V. Gruznev, A. N. Mihalyuk, C. M. Wei, Y. L. Wang, A. A. Saranin

    We discovered a set of C60 nanostructures that appear to be constructed using a universal building block made of four C60 molecules on Si(111) or Ge(111) surfaces covered by an atomic layer of Tl, Pb, or their compound. The building block is a four-C60 cluster having a shape reminiscent of the three-petal flower “white trillium.” Therefore, we call it “trilliumon” and the various 2D ordered nanostructures derived from it “trilliumenes.” Self-assembly of the trilliumenes is a result of an intricate interplay among the adsorbed C60 molecules, metal atoms, and semiconductor substrates. Remarkably, all metal layers triggering formation of trilliumenes on the Si(111) surface have recently been reported to be the thinnest 2D superconductors. In this respect, the trilliumenes show promise to be 2D nanostructured superconductors whose properties are awaiting their exploration.

    更新日期:2018-07-21
  • Chirality at two-dimensional surfaces: A perspective from small molecule alcohol assembly on Au(111)
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-18
    Melissa L. Liriano, Amanda M. Larson, Chiara Gattinoni, Javier Carrasco, Ashleigh E. Baber, Emily A. Lewis, Colin J. Murphy, Timothy J. Lawton, Matthew D. Marcinkowski, Andrew J. Therrien, Angelos Michaelides, E. Charles H. Sykes

    The delicate balance between hydrogen bonding and van der Waals interactions determines the stability, structure, and chirality of many molecular and supramolecular aggregates weakly adsorbed on solid surfaces. Yet the inherent complexity of these systems makes their experimental study at the molecular level very challenging. In this quest, small alcohols adsorbed on metal surfaces have become a useful model system to gain fundamental insight into the interplay of such molecule-surface and molecule-molecule interactions. Here, through a combination of scanning tunneling microscopy and density functional theory, we compare and contrast the adsorption and self-assembly of a range of small alcohols from methanol to butanol on Au(111). We find that longer chained alcohols prefer to form zigzag chains held together by extended hydrogen bonded networks between adjacent molecules. When alcohols bind to a metal surface datively via one of the two lone electron pairs of the oxygen atom, they become chiral. Therefore, the chain structures are formed by a hydrogen-bonded network between adjacent molecules with alternating adsorbed chirality. These chain structures accommodate longer alkyl tails through larger unit cells, while the position of the hydroxyl group within the alcohol molecule can produce denser unit cells that maximize intermolecular interactions. Interestingly, when intrinsic chirality is introduced into the molecule as in the case of 2-butanol, the assembly changes completely and square packing structures with chiral pockets are observed. This is rationalized by the fact that the intrinsic chirality of the molecule directs the chirality of the adsorbed hydroxyl group meaning that heterochiral chain structures cannot form. Overall this study provides a general framework for understanding the effect of simple alcohol molecular adstructures on hydrogen bonded aggregates and paves the way for rationalizing 2D chiral supramolecular assembly.

    更新日期:2018-07-21
  • Effects of the cooperative interaction on the diffusion of hydrogen on MgO(100)
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-20
    Ivano E. Castelli, Stefan G. Soriga, Isabela C. Man

    Understanding hydrogen diffusion is important for applications such as hydrogen storage and spillover materials. On semiconductors, where paired electron acceptors and donors stabilize each other, the hydrogen diffusion depends on the number of adsorbed fragments. Using density functional theory, we investigate the effects of preadsorbed hydrogens on activation energy and reaction path for hydrogen diffusion on MgO(100): the presence of an unpaired hydrogen causes a diffusion, on O-sites, above the surface with a lower activation energy compared to the case of paired hydrogens where the diffusion distorts the surface. This effect is missing for diffusion on Mg-sites.

    更新日期:2018-07-21
  • Many-particle mobility and diffusion tensors for objects in viscous sheets
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-19
    Yulia Sokolov, Haim Diamant

    We derive a mobility tensor for many cylindrical objects embedded in a viscous sheet. This tensor guarantees a positive dissipation rate for any configuration of particles and forces, analogous to the Rotne-Prager-Yamakawa tensor for spherical particles in a three-dimensional viscous fluid. We test our result for a ring of radially driven particles, demonstrating the positive-definite property at all particle densities. The derived tensor can be utilized in Brownian dynamics simulations with hydrodynamic interactions for such systems as proteins in biomembranes and inclusions in free-standing liquid films.

    更新日期:2018-07-21
  • A spin-1 representation for dual-funnel energy landscapes
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-20
    Justin E. Elenewski, Kirill A. Velizhanin, Michael Zwolak

    The interconversion between the left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue. We explore this possibility using all-atom replica exchange molecular dynamics and an Ising-like model, demonstrating that the energy landscape architecture is at odds with a two-state picture. A three-state model—left, right, and unstructured—can account for most key intermediates during chiral interconversion. Competing folds and excited conformational states still impose limitations on the scope of this approach. However, the improvement is stark: Moving from a two-state to a three-state model decreases the fit error from 1.6 kBT to 0.3 kBT along the left-to-right interconversion pathway.

    更新日期:2018-07-21
  • Perspective: Basic understanding of condensed phases of matter via packing models
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-10
    S. Torquato

    Packing problems have been a source of fascination for millennia and their study has produced a rich literature that spans numerous disciplines. Investigations of hard-particle packing models have provided basic insights into the structure and bulk properties of condensed phases of matter, including low-temperature states (e.g., molecular and colloidal liquids, crystals, and glasses), multiphase heterogeneous media, granular media, and biological systems. The densest packings are of great interest in pure mathematics, including discrete geometry and number theory. This perspective reviews pertinent theoretical and computational literature concerning the equilibrium, metastable, and nonequilibrium packings of hard-particle packings in various Euclidean space dimensions. In the case of jammed packings, emphasis will be placed on the “geometric-structure” approach, which provides a powerful and unified means to quantitatively characterize individual packings via jamming categories and “order” maps. It incorporates extremal jammed states, including the densest packings, maximally random jammed states, and lowest-density jammed structures. Packings of identical spheres, spheres with a size distribution, and nonspherical particles are also surveyed. We close this review by identifying challenges and open questions for future research.

    更新日期:2018-07-14
  • Communication: Adiabatic quantum trajectory capture for cold and ultra-cold chemical reactions
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-13
    Yohann Scribano, Gérard Parlant, Bill Poirier

    The Langevin capture model is often used to describe barrierless reactive collisions. At very low temperatures, quantum effects may alter this simple capture image and dramatically affect the reaction probability. In this paper, we use the trajectory-ensemble reformulation of quantum mechanics, as recently proposed by one of the authors (Poirier) to compute adiabatic-channel capture probabilities and cross-sections for the highly exothermic reaction Li + CaH(v = 0, j = 0) → LiH + Ca, at low and ultra-low temperatures. Each captured quantum trajectory takes full account of tunneling and quantum reflection along the radial collision coordinate. Our approach is found to be very fast and accurate, down to extremely low temperatures. Moreover, it provides an intuitive and practical procedure for determining the capture distance (i.e., where the capture probability is evaluated), which would otherwise be arbitrary.

    更新日期:2018-07-14
  • Pore diameter dependence of catalytic activity: p-nitrobenzaldehyde conversion to an aldol product in amine-functionalized mesoporous silica
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-09
    Andres García, Igor I. Slowing, James W. Evans

    The reaction yield for conversion of p-nitrobenzaldehyde (PNB) to an aldol product in amine-functionalized mesoporous silica nanoparticles (MSN) exhibits a 20-fold enhancement for a modest increase in pore diameter, d. This enhanced catalytic activity is shown to reflect a strong increase in the “passing propensity,” P, of reactant and product species inside the pores. We find that P ≈ 0, corresponding to single-file diffusion, applies for the smallest d which still significantly exceeds the linear dimensions of PNB and the aldol product. However, in this regime of narrow pores, these elongated species must align with each other and with the pore axis in order to pass. Thus, P reflects both translational and rotational diffusion. Langevin simulation accounting for these features is used to determine P versus d. The results are also augmented by analytic theory for small and large d where simulation is inefficient. The connection with the catalytic activity and yield is achieved by the incorporation of results for P into a multi-scale modeling framework. Specifically, we apply a spatially coarse-grained (CG) stochastic model for the overall catalytic reaction-diffusion process in MSN. Pores are treated as linear arrays of cells from the ends of which species adsorb and desorb, and between which species hop and exchange, with the exchange rate reflecting P. CG model predictions including yield are assessed by Kinetic Monte Carlo simulation.

    更新日期:2018-07-14
  • Theory of curvature-dependent kinetics of diffusion-limited reactions and its application to ligand binding to a sphere with multiple receptors
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-10
    Changsun Eun

    We present a simple theory that explains how surface curvature affects the reaction kinetics of diffusion-limited reactions on spherically curved surfaces. In this theory, we derive a quadratic equation under the conditions that the rate constant satisfies the Hill and Smoluchowski rate constants at the lowest and highest curvatures, respectively, and that at a certain intermediate curvature, there should be a maximum value of the rate constant, which was recently found in our previous work. We find that the result obtained from our theory is in good agreement with the corresponding one obtained from numerical calculation. In addition, we show that our theory can be directly applied to the Šolc-Stockmayer model of axially symmetric reactants, which can be considered as a spherical reactant with a single reaction site. Furthermore, we discuss using our theory to improve the formula for the rate constant in the Berg-Purcell ligand-binding model of a cell membrane covered by multiple receptors. Our simple theory yields insight into the effect of curvature on diffusion-influenced reactions and provides a useful formula for easily and quantitatively evaluating the curvature effect.

    更新日期:2018-07-14
  • Relation between image charge and potential alignment corrections for charged defects in periodic boundary conditions
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-11
    T. R. Durrant, S. T. Murphy, M. B. Watkins, A. L. Shluger

    Charged defects are often studied within the periodic density functional theory (DFT), but this introduces strong finite-size artifacts. In this work, we develop an electrostatic image interaction correction (IIC) method based on the direct solution of the Poisson equation for charge models constructed directly from DFT calculations. These IICs are found to be detail-insensitive, depending almost entirely on bulk dielectric properties. As these IICs are not able to fully explain the observed finite-size scaling, we explore potential alignment in detail and introduce a novel decomposition to separate out different contributions. We find that the two main sources of potential alignment are defect image interactions and changes in the number of atoms present in the supercell. This first effect is accurately predicted by the periodic part of our IIC. The second contribution is unrelated to the IIC and justifies the common observation that the magnitude of finite-size dependence can strongly vary between vacancy and interstitial defects. It can be approximately predicted using atomic radius, but is strongly sensitive to the pseudopotential employed. Combined, these developments provide a new justification for known finite-size scaling rules. Our results suggest that for cubic supercells, the Lany-Zunger IIC, combined with simplified potential alignment between neutral systems, can yield accurate corrections in spite of the simplicity of the approach.

    更新日期:2018-07-14
  • Adaptive resolution molecular dynamics technique: Down to the essential
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-12
    Christian Krekeler, Animesh Agarwal, Christoph Junghans, Matej Praprotnik, Luigi Delle Site

    We investigate the role of the thermodynamic (TD) force as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution molecular dynamics setup assures thermodynamic equilibrium between atomistically resolved and coarse-grained regions, allowing the proper exchange of molecules. We numerically prove that indeed for systems as relevant as liquid water and 1,3-dimethylimidazolium chloride ionic liquid, the combined action of the TD force and thermostat allows for computationally efficient and numerically accurate simulations, beyond the current capabilities of adaptive resolution setups, which employ switching functions in the coupling region.

    更新日期:2018-07-14
  • Linear response time-dependent density functional theory without unoccupied states: The Kohn-Sham-Sternheimer scheme revisited
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-12
    Fabian Hofmann, Ingo Schelter, Stephan Kümmel

    The Sternheimer approach to time-dependent density functional theory in the linear response regime is attractive because of its computational efficiency. The latter results from avoiding the explicit calculation of unoccupied orbitals and from the basic structure of the Sternheimer equations, which naturally lend themselves to far-reaching parallelization. In this article, we take a fresh look at the frequency-dependent Sternheimer equations. We first give a complete, self-contained derivation of the equations that complements previous derivations. We then discuss several aspects of an efficient numerical realization. As a worked example, we compute the photoabsorption spectra of small hydrogenated silicon clusters and confirm that for these the quality of the Kohn-Sham eigenvalues is more important than the effects of the exchange-correlation kernel. Finally, we demonstrate how triplet excitations can readily be computed from the Sternheimer approach.

    更新日期:2018-07-14
  • State-interaction pair-density functional theory
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-13
    Andrew M. Sand, Chad E. Hoyer, Donald G. Truhlar, Laura Gagliardi

    The accurate description of ground- and excited-state potential energy surfaces poses a challenge for many electronic structure methods, especially in regions where strong electronic state interaction occurs. Here we introduce a new methodology, state-interaction pair-density functional theory (SI-PDFT), to target molecular systems exhibiting strong interaction of electronic states. SI-PDFT is an extension of multiconfiguration pair-density functional theory in which a set of N electronic states is generated through the diagonalization of an N × N effective Hamiltonian. We demonstrate the accuracy of the method by performing calculations on the ionic–neutral avoided crossing in lithium fluoride and the 1ππ-1πσ* avoided crossing in the H—O bond photodissociation in phenol. We show that SI-PDFT can be a useful tool in the study of photochemistry and nonadiabatic dynamics.

    更新日期:2018-07-14
  • Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-13
    Tim J. Zuehlsdorff, Joseph A. Napoli, Joel M. Milanese, Thomas E. Markland, Christine M. Isborn

    Many physical phenomena must be accounted for to accurately model solution-phase optical spectral line shapes, from the sampling of chromophore-solvent configurations to the electronic-vibrational transitions leading to vibronic fine structure. Here we thoroughly explore the role of nuclear quantum effects, direct and indirect solvent effects, and vibronic effects in the computation of the optical spectrum of the aqueously solvated anionic chromophores of green fluorescent protein and photoactive yellow protein. By analyzing the chromophore and solvent configurations, the distributions of vertical excitation energies, the absorption spectra computed within the ensemble approach, and the absorption spectra computed within the ensemble plus zero-temperature Franck-Condon approach, we show how solvent, nuclear quantum effects, and vibronic transitions alter the optical absorption spectra. We find that including nuclear quantum effects in the sampling of chromophore-solvent configurations using ab initio path integral molecular dynamics simulations leads to improved spectral shapes through three mechanisms. The three mechanisms that lead to line shape broadening and a better description of the high-energy tail are softening of heavy atom bonds in the chromophore that couple to the optically bright state, widening the distribution of vertical excitation energies from more diverse solvation environments, and redistributing spectral weight from the 0-0 vibronic transition to higher energy vibronic transitions when computing the Franck-Condon spectrum in a frozen solvent pocket. The absorption spectra computed using the combined ensemble plus zero-temperature Franck-Condon approach yield significant improvements in spectral shape and width compared to the spectra computed with the ensemble approach. Using the combined approach with configurations sampled from path integral molecular dynamics trajectories presents a significant step forward in accurately modeling the absorption spectra of aqueously solvated chromophores.

    更新日期:2018-07-14
  • Nonlinear-response properties in a simplified time-dependent density functional theory (sTD-DFT) framework: Evaluation of the first hyperpolarizability
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-13
    Marc de Wergifosse, Stefan Grimme

    Recent developments in nonlinear imaging microscopy show the need to implement new theoretical tools, which are able to characterize nonlinear optical properties in an efficient way. For second-harmonic imaging microscopy (SHIM), quantum chemistry could play an important role to design new exogenous dyes with enhanced first hyperpolarizabilities or to characterize the response origin in large endogenous biological systems. Such methods should be able to screen a large number of compounds while reproducing their trends and to treat large systems in reasonable computation times. To fulfill these requirements, we present a new simplified time-dependent density functional theory (sTD-DFT) implementation to evaluate the first hyperpolarizability where the Coulomb and exchange integrals are approximated by short-range damped Coulomb interactions of transition density monopoles. For an ultra-fast computation of the first hyperpolarizability, a tight-binding version (sTD-DFT-xTB) is also proposed. In our implementation, a sTD-DFT calculation is more than 600 time faster with respect to a regular TD-DFT treatment, while the xTB version speeds up the entire calculation further by at least two orders of magnitude. We challenge our implementation on three test cases: typical push-pull π-conjugated compounds, fluorescent proteins, and a collagen model, which were selected to model requirements for SHIM applications.

    更新日期:2018-07-14
  • Laser-induced fluorescence detection of the elusive SiCF free radical
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-09
    Gretchen Rothschopf, Tony C. Smith, Dennis J. Clouthier

    The SiCF free radical has been spectroscopically identified for the first time. The radical was produced in an electric discharge jet using CF3Si(CH3)3 or CF3SiH3 vapor in high pressure argon as the precursor. The laser-induced fluorescence spectrum of the Ã∑+2−X̃∏2 band system in the 610 − 550 nm region was recorded and the ∏3/22 spin component of the 0—0 band was studied at high resolution. Rotational analysis gave the B values for the combining states, and by fixing the CF bond lengths at ab initio values we obtained r″Si–C=1.6921Å and r′Si–C=1.594(1)Å. The bond lengths correspond to a silicon-carbon double bond in the ground state and an unusual Si−C triple bond in the excited state. Single vibronic level emission spectra yielded the ground state bending and stretching energy levels. These were fitted to a Renner-Teller model that included spin-orbit and limited vibrational anharmonicity effects.

    更新日期:2018-07-14
  • Using reduced density matrix techniques to capture static and dynamic correlation in the energy landscape for the decomposition of the CH2CH2ONO radical and support a non-IRC pathway
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-10
    Scott E. Smart, Preston G. Scrape, Laurie J. Butler, David A. Mazziotti

    The unexpected abundance of HNO in the photodecomposition of the radical 2-nitrosooxy ethyl (CH2CH2ONO) is investigated through calculations of the potential energy surface by the anti-Hermitian contracted Schrödinger equation (ACSE) method, which directly generates the 2-electron reduced density matrix. The ACSE, which is able to balance single-reference (dynamic) and multi-reference (static) correlation effects, reveals some subtle correlation effects along the intrinsic reaction coordinate (IRC) en route to NO + oxirane, an IRC which offers a potential bifurcation to the HNO + vinoxy product channel. These effects were not fully captured by either single-reference techniques, such as coupled cluster, or multi-reference techniques, such as second-order multi-reference perturbation theory. These correlation effects reveal small to moderate energy changes in key transition states, which have implications for the reaction mechanism as related to the production of HNO.

    更新日期:2018-07-14
  • Rovibrational analysis of c-SiC2H2: Further evidence for out-of-plane bending issues in correlated methods
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-11
    Ryan C. Fortenberry, Carlie M. Novak, Timothy J. Lee

    While the issue of properly describing the out-of-plane bends (OPBs) in sp2 hybridized carbon atoms has reappeared for c-SiC2H2, the present quantum chemical study provides a new characterization of this molecule in order to aid in its potential detection in astrophysically relevant studies. Combining the previous, high-level approach with MP2-F12/aug-cc-pVDZ gives exceptionally accurate results for the comparison of experimental rotational constants and seemingly reliable vibrational frequencies. Most notably, the brightest fundamental vibrational frequency in c-SiC2H2, the b1 OPB, is predicted to lie at 673.4 cm−1, within 4.0 cm−1 of the previous matrix isolation experiment. As with c-C3H2, CCSD(T)-F12/aug-cc-pVTZ appears to be quite susceptible to over estimating the OPB anharmonic correction in c-SiC2H2 and may also do such for in-plane bends, as well. MP2-F12/aug-cc-pVDZ is less susceptible to these errors, and increasing the step size reduces this positive anharmonicity issue in both the cases. The OPB underestimation, however, likely still remains. Finally, estimates for some anharmonic vibrational frequencies are provided for the methylated form, c-SiC2HCH3, which is likely also a product of gas phase reactions of ·SiH with various alkynes.

    更新日期:2018-07-14
  • Structures and spectroscopy of the ammonia eicosamer, (NH3)n=20
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-12
    Alhadji Malloum, Jean Jules Fifen, Jeanet Conradie

    In this work, we reported structures and relative stabilities of the neutral ammonia eicosamer at the APFD/6-31++g(d,p) level of theory. Furthermore, we have examined the temperature dependence isomer distribution and reported the relative population of the ammonia eicosamer for temperatures ranging from 20 to 400 K. Moreover, a theoretical infrared (IR) spectroscopic study is performed to confirm our results. As a result, several stable structures have been identified as isomers of the ammonia eicosamer. The most stable structure is a cage-like isomer with two central solvated ammonia molecules. It is found that cage-like isomers with central solvated ammonia molecules are more stable than other types of structures. Besides, two fused tetrameric cyclic structures belonging to the C2 symmetry point group are also located. Moreover, other reported isomers exhibit an amorphous behavior with no definite symmetry. When considering the temperature dependence isomer distribution, we found that only cage-like isomers contribute to the population of the ammonia eicosamer. The most stable isomer dominates the population of the cluster for all the investigated temperatures. Our analysis shows that only the IR spectra of isomers that contribute to the relative population have their peaks in agreement with the experiment. This agreement could be an indication of the reliability of our proposed structures of the ammonia eicosamer and their relative stability.

    更新日期:2018-07-14
  • Spectroscopy of gold atoms and gold oligomers in helium nanodroplets
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-12
    Roman Messner, Alexander Schiffmann, Johann V. Pototschnig, Maximilian Lasserus, Martin Schnedlitz, Florian Lackner, Wolfgang E. Ernst

    The 6p 2P1/2 ← 6s 2S1/2 and 6p 2P3/2 ← 6s 2S1/2 transitions (D lines) of gold atoms embedded in superfluid helium nanodroplets have been investigated using resonant two-photon ionization spectroscopy. Both transitions are strongly blue-shifted and broadened due to the repulsive interaction between the Au valence electron and the surrounding helium. The in-droplet D lines are superimposed by the spectral signature of Au atoms relaxed into the metastable 2D states. These features are narrower than the in-droplet D lines and exhibit sharp rising edges that coincide with bare atom transitions. It is concluded that they originate from metastable 2D state AuHen exciplexes that have been ejected from the helium droplets during a relaxation process. Interestingly, the mechanism that leads to the formation of these complexes is suppressed for very large helium droplets consisting of about 2 × 106 He atoms, corresponding to a droplet diameter on the order of 50 nm. The assignment of the observed spectral features is supported by ab initio calculations employing a multiconfigurational self-consistent field method and a multi-reference configuration interaction calculation. For large helium droplets doped with Au oligomers, excitation spectra for mass channels corresponding to Aun with n = 2, 3, 4, 5, 7, and 9 are presented. The mass spectrum reveals even-odd oscillations in the number of Au atoms that constitute the oligomer, which is characteristic for coinage metal clusters. Resonances are observed close by the in-droplet D1 and D2 transitions, and the corresponding peak forms are very similar for different oligomer sizes.

    更新日期:2018-07-14
  • Structures of lithium-zinc compounds at high pressures
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-13
    Philip Dalladay-Simpson, Jack Binns, Mengnan Wang, Miriam Peña-Alvarez, Edward J. Pace, Eugene Gregoryanz, Xiao-Jia Chen, Ross Howie

    Intermetallic lithium compounds have found a wide range of applications owing to their light mass and desirable electronic and mechanical properties. Here, by compressing pure lithium and zinc mixtures in a diamond-anvil cell, we observe a direct reaction forming the stoichiometric compound LiZn, at pressures below 1 GPa. On further compression above 10 GPa, we observe the formation of Li2Zn, which is the highest lithium content compound to be discovered in the Li–Zn system. Our results constrain the structures of these compounds and their evolution with pressure, furthering our understanding of potentially useful light volume-efficient energy storage materials.

    更新日期:2018-07-14
  • Accurate rovibrational energies of ozone isotopologues up to J = 10 utilizing artificial neural networks
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-13
    Corey Petty, Rene F. K. Spada, Francisco B. C. Machado, Bill Poirier

    In recent years, ozone and its isotopologues have been a topic of interest in many fields of research, due to its importance in atmospheric chemistry and its anomalous isotopic enrichment—or the so-called “mass-independent fractionation.” In the field of potential energy surface (PES) creation, debate over the existence of a potential barrier just under the dissociation threshold (referred to as a “potential reef”) has plagued research for some years. Recently, Dawes and co-workers [Dawes, Lolur, Li, Jiang, and Guo (DLLJG) J. Chem. Phys. 139, 201103 (2013)] created a highly accurate global PES, for which the reef is found to be replaced with a (monotonic) “plateau.” Subsequent dynamical calculations on this “DLLJG” PES have shown improved agreement with experiment, particularly the vibrational spectrum. However, it is well known that reaction dynamics is also highly influenced by the rovibrational states, especially in cases like ozone that assume a Lindemann-type mechanism. Accordingly, we present the first significant step toward a complete characterization of the rovibrational spectrum for various isotopologues of ozone, computed using the DLLJG PES together with the ScalIT suite of parallel codes. Additionally, artificial neural networks are used in an innovative fashion—not to construct the PES function per se but rather to greatly speed up its evaluation.

    更新日期:2018-07-14
  • Possible universal relation between short time β-relaxation and long time α-relaxation in glass-forming liquids
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-11
    Rajsekhar Das, Indrajit Tah, Smarajit Karmakar

    Relaxation processes in supercooled liquids are known to exhibit interesting complex behavior. One of the hallmarks of this relaxation process observed in the measured auto correlation function is the occurrence of multiple steps of relaxations. The shorter time relaxation is known as the β-relaxation which is believed to be due to the motion of particles in the cage formed by their neighbors. The longer time relaxation is called the α-relaxation. The time scales of these two relaxations processes dramatically separate out with supercooling. In spite of decades of research, it is still not clearly known how these relaxation processes are related to each other. In this work, we show that there is a possible universal relation between short time β-relaxation and long time α-relaxation. We also show that the proposed relation can be rationalized within random first order transition theory of glass transition if power law relation is assumed between static and dynamic length scales.

    更新日期:2018-07-14
  • Electronic response of aluminum-bearing minerals
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-12
    Micah P. Prange, Xin Zhang, Eugene S. Ilton, Libor Kovarik, Mark H. Engelhard, Sebastien N. Kerisit

    Aluminum-bearing minerals show different hydrogen evolution and dissolution properties when subjected to radiation, but the complicated sequence of events following interaction with high-energy radiation is not understood. To gain insight into the possible mechanisms of hydrogen production in nanoparticulate minerals, we study the electronic response and determine the bandgap energies of three common aluminum-bearing minerals with varying hydrogen content: gibbsite (Al(OH)3), boehmite (AlOOH), and alumina (Al2O3) using electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and first-principles electronic structure calculations employing hybrid density functionals. We find that the amount of hydrogen has only a small effect on the number and spectrum of photoexcitations in this class of materials. Electronic structure calculations demonstrate that low energy electrons are isotropically mobile, while holes in the valence band are likely constrained to move in layers. Furthermore, holes in the valence band of boehmite are found to be significantly more mobile than those in gibbsite, suggesting that the differences in radiolytic and dissolution behavior are related to hole transport.

    更新日期:2018-07-14
  • The race within supercooled liquids—Relaxation versus crystallization
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-13
    Edgar D. Zanotto, Daniel R. Cassar

    Can any liquid be cooled down below its melting point to an isentropic (Kauzmann) temperature without vitrifying or crystallizing? This long-standing question concerning the ultimate fate of supercooled liquids is one of the key problems in condensed matter physics and materials science. In this article, we used a plethora of thermodynamic and kinetic data and well established theoretical models to estimate the kinetic spinodal temperature, TKS (the temperature where the average time for the first critical crystalline nucleus to appear becomes equal to the average relaxation time of a supercooled liquid), and the Kauzmann temperature, TK, for two substances. We focused our attention on selected compositions of the two most important oxide glass-forming systems: a borate and a silicate—which show measurable homogeneous crystal nucleation in laboratory time scales—as proxies of these families of glass-formers. For both materials, we found that the TKS are significantly higher than the predicted TK. Therefore, at ambient pressure, at deep supercoolings before approaching TK, crystallization wins the race over structural relaxation. Hence, the temperature of entropy catastrophe predicted by Kauzmann cannot be reached for the studied substances; it is averted by incipient crystal nucleation. Our finding that TKS > TK for two real glasses corroborate the results of computer simulations for a pressurized silica glass.

    更新日期:2018-07-14
  • Precipitation strengthening in Cu–Ni–Si alloys modeled with ab initio based interatomic potentials
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-09
    Stephen Hocker, Hansjörg Lipp, Eugen Eisfeld, Siegfried Schmauder, Johannes Roth

    Effective interaction potentials suitable for Cu/δ–Ni2Si and Cu/β–Ni3Si are developed. We optimise the potential parameters of an embedded atom method potential to reproduce forces, energies, and stresses obtained from ab initio calculations. Details of the potential generation are given, and its validation is demonstrated. The potentials are used in molecular dynamics simulations of shear tests to study the interactions of edge dislocations with coherent δ–Ni2Si and β–Ni3Si precipitates embedded in a copper matrix. In spite of significantly different crystallographic structures of copper and δ–Ni2Si which usually result in circumvention of dislocations, we also observed cutting processes in our simulations. Dislocations cut for a specific orientation of the δ–Ni2Si precipitate and in some cases where dislocation loops originating from previous circumvention processes are present in the glide plane. It is found that β–Ni3Si precipitates have a similar effect on precipitation strengthening as δ–Ni2Si. Dislocations usually cut β–Ni3Si but increased coherency strain can lead to circumvention processes.

    更新日期:2018-07-14
  • Two-dimensional Au-1,3,5 triethynylbenzene organometallic lattice: Structure, half-metallicity, and gas sensing
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-09
    Junfeng Zheng, Jiongyue Hao, Faling Ling, Huirong Jing, Yankun Chen, Tingwei Zhou, Liang Fang, Qian Chen, Miao Zhou

    On the basis of first-principles calculations, we investigated the structural and electronic properties of the two-dimensional (2D) Au-1,3,5 triethynylbenzene (Au-TEB) framework, which has been recently synthesized by homocoupling reactions in experiments. Featured by the C-Au-C linkage, the 2D Au-TEB network has a kagome lattice by Au atoms and a hexagonal lattice by organic molecules within the same metal-organic framework (MOF), which exhibits intrinsic half-metallicity with one spin channel metallic and the other spin channel fully insulating with a large energy gap of 2.8 eV. Two branches of kagome bands are located near the Fermi level, with each branch including one flat band and two Dirac bands, which originates from the out-of-plane dxz and dyz orbitals of Au and may lead to many exotic topological quantum phases. We further studied the adsorption of F atoms, Cl atoms, and small gas molecules including O2, CO, NO2, and NH3 on the Au-TEB network, aiming to exploit its potential applications in gas sensors. Detailed analyses on adsorption geometry, energy, molecular orbital interaction, and electronic structure modification suggest the great potential of Au-TEP as a promising alternative for gas sensing. We expect these results to expand the universe of low-dimensional half-metallic MOF structures and shed new light on their practical applications in nanoelectronics/spintronics.

    更新日期:2018-07-14
  • Molecular mechanism of charge inversion revealed by polar orientation of interfacial water molecules: A heterodyne-detected vibrational sum frequency generation study
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-11
    Matthew M. Sartin, Woongmo Sung, Satoshi Nihonyanagi, Tahei Tahara

    “Charge inversion” is a phenomenon in which multivalent counterions overcompensate for interfacial charges and invert the sign of the net charge near a surface. This phenomenon is believed to be relevant to biologically important processes such as DNA condensation, and hence it has attracted much attention. We investigated the polar orientation of interfacial water molecules at two different negatively charged interfaces in the absence and presence of La3+ using heterodyne-detected vibrational sum frequency generation spectroscopy, which can directly determine the up/down orientation of interfacial molecules. It was found that the orientations of water molecules at a bio-relevant phospholipid interface change from the hydrogen-up to the hydrogen-down with the addition of 10 µM La3+. This change of water orientation indicates that the net charge at the phospholipid interface is inverted by adsorption of La3+ to the phosphate headgroup. By contrast, at an alkylsulfate interface, the majority of the interfacial water molecules remain hydrogen-up orientated even in the presence of 25 mM La3+, indicating that the sulfate headgroup is still solvated by up-oriented water. The observed headgroup specificity suggests that charge inversion at the phospholipid interface originates primarily from the chemical interaction between the phosphate and La3+ ion.

    更新日期:2018-07-14
  • Saltwater transport through pristine and positively charged graphene membranes
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-12
    Chinh Thanh Nguyen, Ali Beskok

    Transport of saltwater through pristine and positively charged single-layer graphene nanoporous membranes is investigated using molecular dynamics simulations. Pressure-driven flows are induced by motion of specular reflecting boundaries at feed and permeate sides with constant speed. Unlike previous studies in the literature, this method induces a desired flow rate and calculates the resulting pressure difference in the reservoirs. Due to the hexagonal structure of graphene, the hydraulic diameters of nano-pores are used to correlate flow rate and pressure drop data. Simulations are performed for three different pore sizes and flow rates for the pristine and charged membrane cases. In order to create better statistical averages for salt rejection rates, ten different initial conditions of Na+ and Cl− distribution in the feed side are used for each simulation case. Using data from 180 distinct simulation cases and utilizing the Buckingham Pi theorem, we develop a functional relationship between the volumetric flow rate, pressure drop, pore diameter, and the dynamic viscosity of saltwater. A linear relationship between the volumetric flow rate and pressure drop is observed. For the same flow rate and pore size, charged membranes exhibit larger pressure drops. Graphene membranes with 9.90 Å pore diameter results in 100% salt rejection with 163.2 l/h cm2 water flux, requiring a pressure drop of 35.02 MPa.

    更新日期:2018-07-14
  • Theoretical study on the polymer translocation into an attractive sphere
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-09
    Li-Zhen Sun, Meng-Bo Luo, Wei-Ping Cao, Haibin Li

    We report a non-sampling model, combining the blob method with the standard lattice-based approximation, to calculate the free energy for the polymer translocation into an attractive sphere (i.e., spherical confined trans side) through a small pore. The translocation time is then calculated by the Fokker-Planck equation based on the free energy profile. There is a competition between the confinement effect of the sphere and the polymer-sphere attraction. The translocation time is increased due to the confinement effect of the sphere, whereas it is reduced by the polymer-sphere attraction. The two effects offset each other at a special polymer-sphere attraction which is dependent on the sphere size, the polymer length, and the driving force. Moreover, the entire translocation process can be divided into an uncrowded stage where the polymer does not experience the confinement effect of the sphere and a crowded stage where the polymer is confined by the sphere. At the critical sphere radius, the durations of the two (uncrowded and crowded) stages are the same. The critical sphere radius R* has a scaling relation with the polymer length N as R* ∼ Nβ. The calculation results show that the current model can effectively treat the translocation of a three-dimensional self-avoiding polymer into the spherical confined trans side.

    更新日期:2018-07-14
  • Influence of hydrodynamic interactions on stratification in drying mixtures
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-07-09
    Antonia Statt, Michael P. Howard, Athanassios Z. Panagiotopoulos

    Nonequilibrium molecular dynamics simulations are used to investigate the influence of hydrodynamic interactions on vertical segregation (stratification) in drying mixtures of long and short polymer chains. In agreement with previous computer simulations and theoretical modeling, the short polymers stratify above the long polymers at the top of the drying film when hydrodynamic interactions between polymers are neglected. However, no stratification occurs under the same drying conditions when hydrodynamic interactions are incorporated through an explicit solvent model. Our analysis demonstrates that models lacking hydrodynamic interactions do not faithfully represent stratification in drying mixtures, in agreement with the recent analysis of an idealized model for diffusiophoresis. Hydrodynamic interactions must be incorporated into such models for drying mixtures in future.

    更新日期:2018-07-14
Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
化学 • 材料 期刊列表