*J Chem Phys ; 152(23): 234108, 2020 Jun 21.*

##### RESUMO

We investigate rates of proton-coupled electron transfer (PCET) in potential sweep experiments for a generalized Anderson-Holstein model with the inclusion of a quantized proton coordinate. To model this system, we utilize a quantum classical Liouville equation embedded inside of a classical master equation, which can be solved approximately with a recently developed algorithm combining diffusional effects and surface hopping between electronic states. We find that the addition of nuclear quantum effects through the proton coordinate can yield quantitatively (but not qualitatively) different IV curves under a potential sweep compared to electron transfer (ET). Additionally, we find that kinetic isotope effects give rise to a shift in the peak potential, but not the peak current, which would allow for quantification of whether an electrochemical ET event is proton-coupled or not. These findings suggest that it will be very difficult to completely understand coupled nuclear-electronic effects in electrochemical voltammetry experiments using only IV curves, and new experimental techniques will be needed to draw inferences about the nature of electrochemical PCET.

*J Chem Phys ; 152(6): 064105, 2020 Feb 14.*

##### RESUMO

We develop several configuration interaction approaches for characterizing the electronic structure of an adsorbate on a metal surface (at least in model form). When one can separate the adsorbate from the substrate, these methods can achieve a reasonable description of adsorbate on-site electron-electron correlation in the presence of a continuum of states. While the present paper is restricted to the Anderson impurity model, there is hope that these methods can be extended to ab initio Hamiltonians and provide insight into the structure and dynamics of molecule-metal surface interactions.

*J Phys Chem A ; 124(5): 757-771, 2020 Feb 06.*

##### RESUMO

Dynamics at molecule-metal interfaces are a subject of intense current interest and come in many different flavors of experiments: gas-phase scattering, chemisorption, electrochemistry, nanojunction transport, and heterogeneous catalysis, to name a few. These dynamics involve nuclear degrees of freedom entangled with many electronic degrees of freedom (in the metal), and as such there is always the possibility for nonadiabatic phenomena to appear: the nuclei do not necessarily need to move slower than the electrons to break the Born-Oppenheimer (BO) approximation. In this Feature Article, we review a set of dynamical methods developed recently to deal with such nonadiabatic phenomena at a metal surface, methods that serve as alternatives to Tully's independent electron surface hopping (IESH) model. In the weak molecule-metal coupling regime, a classical master equation (CME) can be derived and a simple surface hopping approach is proposed to propagate nuclear and electronic dynamics stochastically. In the strong molecule-metal interaction regime, a Fokker-Planck equation can be derived for the nuclear dynamics, with electronic DoFs incorporated into the overall friction and random force. Lastly, a broadened classical master equation (BCME) can interpolate between the weak and strong molecule-metal interactions. Here, we briefly review these methods and the relevant benchmarking data, showing in particular how the methods can be used to calculate nonequilibrium transport properties. We highlight several open questions and pose several avenues for future study.

*J Chem Theory Comput ; 15(12): 6703-6711, 2019 Dec 10.*

##### RESUMO

We develop a stochastic resolution of identity approach to the real-time second-order Green's function (real-time sRI-GF2) theory, extending our recent work for imaginary-time Matsubara Green's function [ Takeshita et al. J. Chem. Phys. 2019 , 151 , 044114 ]. The approach provides a framework to obtain the quasi-particle spectra across a wide range of frequencies and predicts ionization potentials and electron affinities. To assess the accuracy of the real-time sRI-GF2, we study a series of molecules and compare our results to experiments as well as to a many-body perturbation approach based on the GW approximation, where we find that the real-time sRI-GF2 is as accurate as self-consistent GW. The stochastic formulation reduces the formal computatinal scaling from O(Ne5) down to O(Ne3) where Ne is the number of electrons. This is illustrated for a chain of hydrogen dimers, where we observe a slightly lower than cubic scaling for systems containing up to Ne ≈ 1000 electrons.

*J Chem Phys ; 151(4): 044114, 2019 Jul 28.*

##### RESUMO

We develop a stochastic resolution of identity representation to the second-order Matsubara Green's function (sRI-GF2) theory. Using a stochastic resolution of the Coulomb integrals, the second order Born self-energy in GF2 is decoupled and reduced to matrix products/contractions, which reduces the computational cost from O(N5) to O(N3) (with N being the number of atomic orbitals). The current approach can be viewed as an extension to our previous work on stochastic resolution of identity second order Møller-Plesset perturbation theory [T. Y. Takeshita et al., J. Chem. Theory Comput. 13, 4605 (2017)] and offers an alternative to previous stochastic GF2 formulations [D. Neuhauser et al., J. Chem. Theory Comput. 13, 5396 (2017)]. We show that sRI-GF2 recovers the deterministic GF2 results for small systems, is computationally faster than deterministic GF2 for N > 80, and is a practical approach to describe weak correlations in systems with 103 electrons and more.

*J Chem Phys ; 151(7): 074113, 2019 Aug 21.*

##### RESUMO

Although the quantum classical Liouville equation (QCLE) arises by cutting off the exact equation of motion for a coupled nuclear-electronic system at order 1 (1 = â0), we show that the QCLE does include Berry's phase effects and Berry's forces (which are proportional to a higher order, â = â1). Thus, the fundamental equation underlying mixed quantum-classical dynamics does not need a correction for Berry's phase effects and is valid for the case of complex (i.e., not just real) Hamiltonians, where exotic features can arise in the course of electronic relaxation. Furthermore, we also show that, even though Tully's surface hopping model ignores Berry's phase, Berry's phase effects are included automatically within Ehrenfest dynamics. These findings should be of great importance if we seek to model coupled nuclear-electronic dynamics for systems with odd numbers of electrons and spin-orbit coupling, where the complex nature of the Hamiltonian is paramount.

*J Chem Phys ; 150(23): 234112, 2019 Jun 21.*

##### RESUMO

We present a strategy for mapping the dynamics of a fermionic quantum system to a set of classical dynamical variables. The approach is based on imposing the correspondence relation between the commutator and the Poisson bracket, preserving Heisenberg's equation of motion for one-body operators. In order to accommodate the effect of two-body terms, we further impose quantization on the spin-dependent occupation numbers in the classical equations of motion, with a parameter that is determined self-consistently. Expectation values for observables are taken with respect to an initial quasiclassical distribution that respects the original quantization of the occupation numbers. The proposed classical map becomes complete under the evolution of quadratic Hamiltonians and is extended for all even order observables. We show that the map provides an accurate description of the dynamics for an interacting quantum impurity model in the coulomb blockade regime, at both low and high temperatures. The numerical results are aided by a novel importance sampling scheme that employs a reference system to reduce significantly the sampling effort required to converge the classical calculations.

*Zhongguo Dang Dai Er Ke Za Zhi ; 21(3): 265-270, 2019 Mar.*

##### RESUMO

OBJECTIVE: To study the clinical effect and safety of tacrolimus (TAC) combined with glucocorticoid (GC) versus mycophenolate mofetil (MMF) combined with GC in the treatment of primary IgA nephropathy (IgAN) in children. METHODS: A retrospective analysis was performed for the clinical data of children with primary IgAN confirmed by renal pathology between January 2012 and December 2017. These children were divided into TAC group and MMF group according to the treatment regimen. Their clinical data before treatment and at 1, 3, and 6 months of treatment were collected, and the remission status of IgAN and adverse reactions were compared between the two groups. RESULTS: A total of 43 children who met the inclusion criteria were enrolled, with 15 children in the TAC group and 28 children in the MMF group. At 1 month of treatment, there was no significant difference in the remission status between the two groups (P>0.05). At 3 and 6 months of treatment, the TAC group had a significantly better remission status than the MMF group (P<0.05). At 1 month of treatment, the TAC group had higher serum albumin levels than the MMF group (P<0.05). Both groups had a significant increase in serum albumin levels at each time point after treatment (P<0.0083) and a significant increase in the glomerular filtration rate (GFR) at 3 and 6 months of treatment (P<0.0083). There was no significant difference in the overall incidence rate of adverse reactions between the two groups (P>0.05), but fungal infection was observed in one child from the TAC group. CONCLUSIONS: TAC combined with GC can effectively reduce urinary protein in children with primary IgAN, and it has a better short-term clinical effect than MMF combined with GC, with good safety.

##### Assuntos

Glomerulonefrite por IGA , Glucocorticoides/uso terapêutico , Tacrolimo/uso terapêutico , Criança , Quimioterapia Combinada , Glomerulonefrite por IGA/tratamento farmacológico , Humanos , Imunossupressores , Ácido Micofenólico , Estudos Retrospectivos*J Chem Phys ; 148(23): 230901, 2018 Jun 21.*

##### RESUMO

Electronic friction is a correction to the Born-Oppenheimer approximation, whereby nuclei in motion experience a drag in the presence of a manifold of electronic states. The notion of electronic friction has a long history and has been (re-)discovered in the context of a wide variety of different chemical and physical systems including, but not limited to, surface scattering events, surface reactions or chemisorption, electrochemistry, and conduction through molecular-(or nano-) junctions. Over the years, quite a few different forms of electronic friction have been offered in the literature. In this perspective, we briefly review these developments of electronic friction, highlighting the fact that we can now isolate a single, unifying form for (Markovian) electronic friction. We also focus on the role of electron-electron interactions for understanding frictional effects and offer our thoughts on the strengths and weaknesses of using electronic friction to model dynamics in general.

*J Chem Phys ; 148(10): 102317, 2018 Mar 14.*

##### RESUMO

We extend the broadened classical master equation (bCME) approach [W. Dou and J. E. Subotnik, J. Chem. Phys. 144, 024116 (2016)] to the case of two electrodes, such that we may now calculate non-equilibrium transport properties when molecules come near metal surfaces and there is both strong electron-nuclear and strong metal-molecule coupling. By comparing against a numerically exact solution, we show that the bCME usually works very well, provided that the temperature is high enough that a classical treatment of nuclear motion is valid. Finally, in the low temperature (quantum) regime, we suggest a means to incorporate broadening effects in the quantum master equation (QME). This bQME works well for fairly low temperatures.

*Mar Pollut Bull ; 126: 540-548, 2018 Jan.*

##### RESUMO

Coupled nitrogen cycling processes can alleviate the negative effects of eutrophication caused by excessive nitrogen load in estuarine ecosystems. The abundance and diversity of nitrifiers and denitrifiers across different environmental gradients were examined in the sediment of Hangzhou Bay. Quantitative PCR and Pearson's correlation analyses suggested that the bacterial ammonia-oxidizers (AOB) were the dominant phylotypes capable of ammonia oxidation, while the nirS-encoding denitrifiers predominated in the denitrification process. Simultaneously, nitrite and pH were found to be the two major factors influencing amoA and nir gene abundances, and the distribution of bacterial communities. Moreover, the ratio of nirS/AOB amoA gene abundance showed negative correlation with nitrite concentration. Fluorescence in situ hybridization further demonstrated that AOB and acetate-denitrifying cells were closely connected and formed obvious aggregates in the sediment. Together, all these results provided us a preliminary insight for coupled nitrification-denitrification processes in the sediment of Hangzhou Bay.

##### Assuntos

Bactérias/isolamento & purificação , Estuários , Sedimentos Geológicos/microbiologia , Acetatos/metabolismo , Amônia/metabolismo , Bactérias/genética , Bactérias/metabolismo , China , Desnitrificação , Eutrofização , Genes Bacterianos , Hibridização in Situ Fluorescente , Nitrificação , Nitritos/análise , Oxirredução*J Chem Phys ; 147(22): 224105, 2017 Dec 14.*

##### RESUMO

Within a 2-D scattering model, we investigate the vibrational relaxation of an idealized molecule colliding with a metal surface. Two perturbative nonadiabatic dynamics schemes are compared: (i) electronic friction (EF) and (ii) classical master equations. In addition, we also study a third approach, (iii) a broadened classical master equation that interpolates between approaches (i) and (ii). Two conclusions emerge. First, even though we do not have exact data to compare against, we find there is strong evidence suggesting that EF results may be spurious for scattering problems. Second, we find that there is an optimal molecule-metal coupling that maximizes vibrational relaxation rates by inducing large nonadiabatic interactions.

*J Chem Theory Comput ; 13(6): 2430-2439, 2017 Jun 13.*

##### RESUMO

For a molecule with multiple electronic orbitals and many nuclear degrees of freedom near a metal surface, there is a natural embedding of the quantum-classical Liouville equation inside a classical master equation (QCLE-CME) to model nonadiabatic dynamics ( J. Chem. Phys. 2016 , 145 , 054102 ). In this paper, we propose a variety of surface hopping algorithms for solving such a QCLE-CME. We find that an augmented surface hopping (A-SH) algorithm works well for propagating such nonadiabatic dynamics (near a metal surface). We expect the present algorithm will be very useful for modeling electrochemical problems in the future.

*Phys Rev Lett ; 119(4): 046001, 2017 Jul 28.*

##### RESUMO

We present a universal expression for the electronic friction as felt by a set of classical nuclear degrees of freedom (DOFs) coupled to a manifold of quantum electronic DOFs; no assumptions are made regarding the nature of the electronic Hamiltonian and electron-electron repulsions are allowed. Our derivation is based on a quantum-classical Liouville equation for the coupled electronic-nuclear motion, followed by an adiabatic approximation whereby electronic transitions are assumed to equilibrate faster than nuclear movement. The resulting form of friction is completely general, but does reduce to previously published expressions for the quadratic Hamiltonian (i.e., Hamiltonians without electronic correlation). At equilibrium, the second fluctuation-dissipation theorem is satisfied and the frictional matrix is symmetric. To demonstrate the importance of electron-electron correlation, we study electronic friction within the Anderson-Holstein model, where a proper treatment of electron-electron interactions shows signatures of a Kondo resonance and a mean-field treatment is completely inadequate.

*J Chem Phys ; 145(5): 054102, 2016 Aug 07.*

##### RESUMO

We present a very general form of electronic friction as present when a molecule with multiple orbitals hybridizes with a metal electrode. To develop this picture of friction, we embed the quantum-classical Liouville equation (QCLE) within a classical master equation (CME). Thus, this article extends our previous work analyzing the case of one electronic level, as we may now treat the case of multiple levels and many electronic molecular states. We show that, in the adiabatic limit, where electron transitions are much faster than nuclear motion, the QCLE-CME reduces to a Fokker-Planck equation, such that nuclei feel an average force as well as friction and a random force-as caused by their interaction with the metallic electrons. Finally, we show numerically and analytically that our frictional results agree with other published results calculated using non-equilibrium Green's functions. Numerical recipes for solving this QCLE-CME will be provided in a subsequent paper.

*J Chem Theory Comput ; 12(9): 4178-83, 2016 Sep 13.*

##### RESUMO

We investigate barrier crossings within the context of the Anderson-Holstein model, as relevant to coupled nuclear-electronic dynamics near a metal surface. Beyond standard electronic friction or conventional surface-hopping dynamics, we show that a broadened classical master equation can recover both the correct nonadiabatic and the correct adiabatic dynamics for a general escape problem (even with possibly multiple escape channels). In the case of a large barrier with only a single escape channel, we also find a surprising conclusion: electronic friction can recover Marcus's nonadiabatic theory of electron transfer in the limit of small molecule-metal couplings. The latter conclusion establishes a hidden connection between Marcus's nonadiabatic theory and Kramer's adiabatic theory of rate constants.

*J Chem Phys ; 144(7): 074109, 2016 Feb 21.*

##### RESUMO

We investigate equilibrium observables for molecules near metals by employing a potential of mean force (PMF) that takes level broadening into account. Through comparison with exact data, we demonstrate that this PMF approach performs quite well, even for cases where molecule-electrode couplings depend on nuclear position. As an application, we reexamine the possibility of hysteresis effects within the Anderson-Holstein model (i.e., an impurity coupled both to a metal surface and a nuclear oscillator). As compared against the standard mean field approach by Galperin et al. [Nano Lett. 5, 125 (2005)], our PMF approach agrees much better with exact results for average electronic populations both at zero and finite temperature; we find, however, that mean field theory can be very useful for predicting the onset of dynamical instabilities, metastable states, and hysteresis.

*J Chem Phys ; 144(2): 024116, 2016 Jan 14.*

##### RESUMO

A broadened classical master equation (BCME) is proposed for modeling nonadiabatic dynamics for molecules near metal surfaces over a wide range of parameter values and with arbitrary initial conditions. Compared with a standard classical master equation-which is valid in the limit of weak molecule-metal couplings-this BCME should be valid for both weak and strong molecule-metal couplings. (The BCME can be mapped to a Fokker-Planck equation that captures level broadening correctly.) Finally, our BCME can be solved with a simple surface hopping algorithm; numerical tests of equilibrium and dynamical observables look very promising.

*Eur J Pediatr ; 175(1): 49-55, 2016 Jan.*

##### RESUMO

UNLABELLED: Henoch-Schönlein purpura (HSP) is a small-vessel disease in children that is often accompanied by kidney damage. Despite many efforts to improve the early assessment of renal injury in HSP patients, effective markers are still lacking. In recent years, the relationship between kidney injury molecule-1 (KIM-1) and tubulointerstitial injury has drawn much attention, especially regarding the diagnostic potential of serum and urinary KIM-1 levels. However, the diagnostic value of KIM-1 for detecting urinary kidney injury in HSP patients is still elusive. Furthermore, the treatment of Henoch-Schönlein purpura nephritis (HSPN) relies on the clinician's experience without performing renal biopsy, so it is important to find an effective biomarker and therapy. In the present study, we investigated the diagnostic value of urinary KIM-1 for early renal injury in HSP patients enrolled in a prospective, single-center study. Urinary KIM-1 levels were measured in 27 patients with HSP, 32 patients with HSPN (21 HSPN patients had undergone renal biopsy), and 16 healthy donors, as normal controls. The HSPN patients were randomly divided to receive either routine therapy (n = 13) or routine treatment combined with creatine phosphate sodium (CP) (n = 19). Urinary KIM-1 levels were significantly greater in the HSP and HSPN groups than those in the healthy control group (P < 0.01), and were significantly greater in the HSPN group than in the HSP group (P < 0.01). The urinary KIM-1 levels decreased significantly after 10-14 days of treatment with CP compared with conventional therapy (P < 0.05). CONCLUSION: Our results demonstrate the diagnostic value of KIM-1 and the therapeutic potential of CP for early renal damage in HSP patients. WHAT IS KNOWN: Urine kidney injury molecule-1 (KIM-1) is a sensitive biomarker for tubulointerstitial injury. Henoch-Schonlein purpura (HSP) usually presents with renal damage. WHAT IS NEW: Our results suggest that the urinary KIM-1 level is a sensitive and specific biomarker for the detection of early renal damage in HSP and may predict the severity of HSP and HSPN. The administration of creatine phosphate sodium (CP) may reduce urinary KIM-1 levels and thus correct the hypoxic condition of the kidney. Preconditioning with CP may also be a useful adjunct for preventing early renal damage in HSPN patients.