- B97-3c: A revised low-cost variant of the B97-D density functional method. [Journal Article]
- JCJ Chem Phys 2018 Feb 14; 148(6):064104
- A revised version of the well-established B97-D density functional approximation with general applicability for chemical properties of large systems is proposed. Like B97-D, it is based on Becke's po...
A revised version of the well-established B97-D density functional approximation with general applicability for chemical properties of large systems is proposed. Like B97-D, it is based on Becke's power-series ansatz from 1997 and is explicitly parametrized by including the standard D3 semi-classical dispersion correction. The orbitals are expanded in a modified valence triple-zeta Gaussian basis set, which is available for all elements up to Rn. Remaining basis set errors are mostly absorbed in the modified B97 parametrization, while an established atom-pairwise short-range potential is applied to correct for the systematically too long bonds of main group elements which are typical for most semi-local density functionals. The new composite scheme (termed B97-3c) completes the hierarchy of "low-cost" electronic structure methods, which are all mainly free of basis set superposition error and account for most interactions in a physically sound and asymptotically correct manner. B97-3c yields excellent molecular and condensed phase geometries, similar to most hybrid functionals evaluated in a larger basis set expansion. Results on the comprehensive GMTKN55 energy database demonstrate its good performance for main group thermochemistry, kinetics, and non-covalent interactions, when compared to functionals of the same class. This also transfers to metal-organic reactions, which is a major area of applicability for semi-local functionals. B97-3c can be routinely applied to hundreds of atoms on a single processor and we suggest it as a robust computational tool, in particular, for more strongly correlated systems where our previously published "3c" schemes might be problematic.
- Orientation-dependent imaging of electronically excited quantum dots. [Journal Article]
- JCJ Chem Phys 2018 Feb 14; 148(6):064701
- We previously demonstrated that we can image electronic excitations of quantum dots by single-molecule absorption scanning tunneling microscopy (SMA-STM). With this technique, a modulated laser beam ...
We previously demonstrated that we can image electronic excitations of quantum dots by single-molecule absorption scanning tunneling microscopy (SMA-STM). With this technique, a modulated laser beam periodically saturates an electronic transition of a single nanoparticle, and the resulting tunneling current modulation ΔI(x0, y0) maps out the SMA-STM image. In this paper, we first derive the basic theory to calculate ΔI(x0, y0) in the one-electron approximation. For near-resonant tunneling through an empty orbital "i" of the nanostructure, the SMA-STM signal is approximately proportional to the electron density φix0,y02of the excited orbital in the tunneling region. Thus, the SMA-STM signal is approximated by an orbital density map (ODM) of the resonantly excited orbital at energy Ei. The situation is more complex for correlated electron motion, but either way a slice through the excited electronic state structure in the tunneling region is imaged. We then show experimentally that we can nudge quantum dots on the surface and roll them, thus imaging excited state electronic structure of a single quantum dot at different orientations. We use density functional theory to model ODMs at various orientations, for qualitative comparison with the SMA-STM experiment. The model demonstrates that our experimentally observed signal monitors excited states, localized by defects near the surface of an individual quantum dot. The sub-nanometer super-resolution imaging technique demonstrated here could become useful for mapping out the three-dimensional structure of excited states localized by defects within nanomaterials.
- Classical coherent two-dimensional vibrational spectroscopy. [Journal Article]
- JCJ Chem Phys 2018 Feb 14; 148(6):064101
- Two-dimensional (2D) ultrafast spectroscopy is a powerful tool for studying the electronic and vibrational structures of complex systems. Unfortunately, the physical interpretation of these experimen...
Two-dimensional (2D) ultrafast spectroscopy is a powerful tool for studying the electronic and vibrational structures of complex systems. Unfortunately, the physical interpretation of these experiments is obscured by conceptual problems in classical response theory, i.e., the divergence of classical nonlinear response functions. We demonstrate that these difficulties are avoided by modeling classical 2D experiments nonperturbatively, illustrating that nonlinear spectroscopy and nonlinear response are not synonymous. Numerical simulations allow a direct comparison between classical and quantum 2D spectra for simple, weakly anharmonic systems relevant to vibrational spectroscopy. We find that nonperturbative classical theory-although differing in quantitative details-accurately captures the key qualitative features of the quantum 2D spectrum, including the separation of the signal into wavevector-selected pathways, formation of cross peaks between coupled vibrational modes, and coherent beating in the signal as a function of waiting time (so-called "quantum beats"). These results are discussed in terms of a simple analytical model which captures the key physical features of classical 2D spectroscopy and provides a link between classical and quantum descriptions. One interesting conclusion from this comparison is that the "coherence" observed in ultrafast spectroscopy may (at least in vibrational experiments) be understood as a purely classical phenomenon, without reference to quantum mechanics.
- Vibrational treatment of the formic acid double minimum case in valence coordinates. [Journal Article]
- JCJ Chem Phys 2018 Feb 14; 148(6):064303
- One single full dimensional valence coordinate HCOOH ground state potential energy surface accurate for both cis and trans conformers for all levels up to 6000 cm-1relative to trans zero point energy...
One single full dimensional valence coordinate HCOOH ground state potential energy surface accurate for both cis and trans conformers for all levels up to 6000 cm-1relative to trans zero point energy has been generated at CCSD(T)-F12a/aug-cc-pVTZ level. The fundamentals and a set of eigenfunctions complete up to about 3120 and 2660 cm-1for trans- and cis-HCOOH, respectively, have been calculated and assigned using the improved relaxation method of the Heidelberg multi-configuration time-dependent Hartree package and an exact expression for the kinetic energy in valence coordinates generated by the TANA program. The calculated trans fundamental transition frequencies agree with experiment to within 5 cm-1. A few reassignments are suggested. Our results discard any cis trans delocalization effects for vibrational eigenfunctions up to 3640 cm-1relative to trans zero point energy.
- Effect of alkaline metal cations on the ionic structure of cryolite melts: Ab-initio NpT MD study. [Journal Article]
- JCJ Chem Phys 2018 Feb 14; 148(6):064501
- Ab initio molecular dynamics simulations in an NpT ensemble have been performed to study the role of alkaline metal cations (Me = Li, Na, K, Rb) on the structure and vibrational properties of melts o...
Ab initio molecular dynamics simulations in an NpT ensemble have been performed to study the role of alkaline metal cations (Me = Li, Na, K, Rb) on the structure and vibrational properties of melts of Me-cryolites (Me3AlF6) at T = 1300 K. In all melts examined in this work, the species AlF52-has been found to be formed at the highest abundance [from 58% (Li) to 70% (Na)] among the Al-containing anionic clusters. The concentration of clusters AlF4-increases with the size of cations while that of anions AlF63-follows the opposite trend and it becomes negligible in the melts of the K- and Rb-cryolites. The computed percentage of the Al atoms participating in the formation of dimers Al2Fm6-mbridged via common F atoms is significant only in the case of Li- and Na-cryolites (16% and 10%, respectively) and the formation of even larger aggregates is found to be unlikely in all four melts. The percentage of the F atoms that are not bound to Al is ∼20% in all four melts and the ions formed by Me+and F-are found to be only short-lived. Vibrational analysis has been performed using the velocity autocorrelation functions computed for the Cartesian and selected internal coordinates describing Raman-active symmetric stretching vibrations of different AlFnspecies. The results of vibrational analysis allowed us to identify trends in the variation of positions and shapes of peaks corresponding to the anionic fragments AlF4-, AlF52-, and AlF63-with the size of cations, and these trends are found to be consistent with those deduced from the available Raman spectroscopy experiments. Our findings represent a new insight into the properties of cryolite melts, which will be useful for the interpretation of experimental data.
- Laser desorption vs. electrospray of polyyne-threaded rotaxanes: Preventing covalent cross-linking and promoting noncovalent aggregation. [Journal Article]
- JCJ Chem Phys 2018 Feb 14; 148(6):064308
- Laser-induced cross-linking of polyynes is successfully hindered when the polyyne is encapsulated as part of a rotaxane and therefore protected by a surrounding macrocycle. When the rotaxane is elect...
Laser-induced cross-linking of polyynes is successfully hindered when the polyyne is encapsulated as part of a rotaxane and therefore protected by a surrounding macrocycle. When the rotaxane is electrosprayed, however, noncovalent aggregate ions are efficiently formed. Aggregates of considerable size (including more than 50 rotaxane molecules with masses beyond 100k Da) and charge states (up to 13 charges and beyond) have been observed. Either protons or sodium cations act as the charge carriers. These aggregates are not formed when the individual components of the rotaxane, i.e., the macrocycle or the polyyne, are separately electrosprayed. This underlines the structural importance of the rotaxane for the aggregate formation. Straightforward force field calculations indicate that the polyyne thread hinders the folding of the macrocycles, which facilitates the bonding interaction between the two components.
- Detection of transient infrared absorption of SO3and 1,3,2-dioxathietane-2,2-dioxide [cyc-(CH2)O(SO2)O] in the reaction CH2OO+SO2. [Journal Article]
- JCJ Chem Phys 2018 Feb 14; 148(6):064301
- We recorded time-resolved infrared absorption spectra of transient species produced on irradiation at 308 nm of a flowing mixture of CH2I2/O2/N2/SO2at 298 K. Bands of CH2OO were observed initially up...
We recorded time-resolved infrared absorption spectra of transient species produced on irradiation at 308 nm of a flowing mixture of CH2I2/O2/N2/SO2at 298 K. Bands of CH2OO were observed initially upon irradiation; their decrease in intensity was accompanied by the appearance of an intense band at 1391.5 cm-1that is associated with the degenerate SO-stretching mode of SO3, two major bands of HCHO at 1502 and 1745 cm-1, and five new bands near >1340, 1225, 1100, 940, and 880 cm-1. The band near 1340 cm-1was interfered by absorption of SO2and SO3, so its band maximum might be greater than 1340 cm-1. SO3in its internally excited states was produced initially and became thermalized at a later period. The rotational contour of the band of thermalized SO3agrees satisfactorily with the reported spectrum of SO3. These five new bands are tentatively assigned to an intermediate 1,3,2-dioxathietane-2,2-dioxide [cyc-(CH2)O(SO2)O] according to comparison with anharmonic vibrational wavenumbers and relative IR intensities predicted for this intermediate. Observation of a small amount of cyc-(CH2)O(SO2)O is consistent with the expected reaction according to the potential energy scheme predicted previously. SO3+HCHO are the major products of the title reaction. The other predicted product channel HCOOH+SO2was unobserved and its branching ratio was estimated to be <5%.
- Accelerated sampling by infinite swapping of path integral molecular dynamics with surface hopping. [Journal Article]
- JCJ Chem Phys 2018 Feb 14; 148(6):064110
- To accelerate the thermal equilibrium sampling of multi-level quantum systems, the infinite swapping limit of a recently proposed multi-level ring polymer representation is investigated. In the infin...
To accelerate the thermal equilibrium sampling of multi-level quantum systems, the infinite swapping limit of a recently proposed multi-level ring polymer representation is investigated. In the infinite swapping limit, the ring polymer evolves according to an averaged Hamiltonian with respect to all possible surface index configurations of the ring polymer and thus connects the surface hopping approach to the mean-field path-integral molecular dynamics. A multiscale integrator for the infinite swapping limit is also proposed to enable efficient sampling based on the limiting dynamics. Numerical results demonstrate the huge improvement of sampling efficiency of the infinite swapping compared with the direct simulation of path-integral molecular dynamics with surface hopping.
- Short-time dynamics of lysozyme solutions with competing short-range attraction and long-range repulsion: Experiment and theory. [Journal Article]
- JCJ Chem Phys 2018 Feb 14; 148(6):065101
- Recently, atypical static features of microstructural ordering in low-salinity lysozyme protein solutions have been extensively explored experimentally and explained theoretically based on a short-ra...
Recently, atypical static features of microstructural ordering in low-salinity lysozyme protein solutions have been extensively explored experimentally and explained theoretically based on a short-range attractive plus long-range repulsive (SALR) interaction potential. However, the protein dynamics and the relationship to the atypical SALR structure remain to be demonstrated. Here, the applicability of semi-analytic theoretical methods predicting diffusion properties and viscosity in isotropic particle suspensions to low-salinity lysozyme protein solutions is tested. Using the interaction potential parameters previously obtained from static structure factor measurements, our results of Monte Carlo simulations representing seven experimental lysoyzme samples indicate that they exist either in dispersed fluid or random percolated states. The self-consistent Zerah-Hansen scheme is used to describe the static structure factor, S(q), which is the input to our calculation schemes for the short-time hydrodynamic function, H(q), and the zero-frequency viscosity η. The schemes account for hydrodynamic interactions included on an approximate level. Theoretical predictions for H(q) as a function of the wavenumber q quantitatively agree with experimental results at small protein concentrations obtained using neutron spin echo measurements. At higher concentrations, qualitative agreement is preserved although the calculated hydrodynamic functions are overestimated. We attribute the differences for higher concentrations and lower temperatures to translational-rotational diffusion coupling induced by the shape and interaction anisotropy of particles and clusters, patchiness of the lysozyme particle surfaces, and the intra-cluster dynamics, features not included in our simple globular particle model. The theoretical results for the solution viscosity, η, are in qualitative agreement with our experimental data even at higher concentrations. We demonstrate that semi-quantitative predictions of diffusion properties and viscosity of solutions of globular proteins are possible given only the equilibrium structure factor of proteins. Furthermore, we explore the effects of changing the attraction strength on H(q) and η.
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- Quantum dynamics of ClH2O-photodetachment: Isotope effect and impact of anion vibrational excitation. [Journal Article]
- JCJ Chem Phys 2018 Feb 14; 148(6):064305
- Photodetachment of the ClH2O-anion is investigated using full-dimensional quantum mechanics on accurate potential energy surfaces of both the anion and neutral species. Detailed analysis of the photo...
Photodetachment of the ClH2O-anion is investigated using full-dimensional quantum mechanics on accurate potential energy surfaces of both the anion and neutral species. Detailed analysis of the photoelectron spectrum and the corresponding wavefunctions reveals that the photodetachment leads to, in the product channel of the exothermic HCl + OH → Cl + H2O reaction, the formation of numerous Feshbach resonances due apparently to slow energy transfer from H2O vibrational modes to the dissociation coordinate. These long-lived resonances can be grouped into two broad peaks in the low-resolution photoelectron spectrum, which is in good agreement with available experiments, and they are assigned to the ground and first excited OH stretching vibrational manifolds of H2O complexed with Cl. In addition, effects of isotope substitution on the photoelectron spectrum were small. Finally, photodetachment of the vibrationally excited ClH2O-in the ionic hydrogen bond mode is found to lead to Feshbach resonances with higher stretching vibrational excitations in H2O.