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arXiv2014

Wertheim and Bjerrum-Tani-Henderson theories for associating fluids: a critical assessment

Two theories for associating fluids recently used to study clustering in models for self-assembling patchy particles, Wertheim's and Bjerrum-Tani-Henderson theories, are carefully compared. We show that, for a fluid allowing only for dimerization, Wertheim theory is equivalent to the Bjerrum-Tani-Henderson theory neglecting intercluster correlations. Nonetheless, while the former theory is able to account for percolation and condensation, the latter is not. For the Bjerrum-Tani-Henderson theory we also rigorously prove the uniqueness of the solution for the cluster's concentrations and the reduction of the system of equations to a single one for a single unknown. We carry out Monte Carlo simulations of two simple models of dimerizing fluids and compare quantitatively the predictions of the two theories with the simulation data.

cond-mat.stat-mech↗

arXiv2014

The Individual and Collective Effects of Exact Exchange and Dispersion Interactions on the Ab Initio Structure of Liquid Water

In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local vdW/dispersion interactions, via a fully self-consistent density-dependent dispersion correction, and approximate nuclear quantum effects (aNQE), via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx, vdW, and aNQE as resulting from a large-scale AIMD simulation of (H$_2$O)$_{128}$ at the PBE0+vdW level of theory, significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, $S_{\rm OO}(Q)$, and corresponding oxygen-oxygen radial distribution function, $g_{\rm OO}(r)$, that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment as demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of the PBE0 hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions.

cond-mat.soft↗

arXiv2014

A diabatic state model for double proton transfer in hydrogen bonded complexes

Four diabatic states are used to construct a simple model for double proton transfer in hydrogen bonded complexes. Key parameters in the model are the proton donor-acceptor separation R and the ratio, D_1/D_2, between the proton affinity of a donor with one and two protons. Depending on the values of these two parameters the model describes four qualitatively different ground state potential energy surfaces, having zero, one, two, or four saddle points. In the limit D_2=D_1 the model reduces to two decoupled hydrogen bonds. As R decreases a transition can occur from a concerted to a sequential mechanism for double proton transfer.

physics.chem-ph↗

arXiv2014

Equation of state for supercooled water at pressures up to 400 MPa

An equation of state is presented for the thermodynamic properties of cold and supercooled water. It is valid for temperatures from the homogeneous ice nucleation temperature up to 300 K and for pressures up to 400 MPa, and can be extrapolated up to 1000 MPa. The equation of state is compared with experimental data for the density, expansion coefficient, isothermal compressibility, speed of sound, and heat capacity. Estimates for the accuracy of the equation are given. The melting curve of ice I is calculated from the phase-equilibrium condition between the proposed equation and an existing equation of state for ice I.

cond-mat.stat-mech↗

arXiv2014

Transition properties from the Hermitian formulation of the coupled cluster polarization propagator

Theory of one-electron transition density matrices has been formulated within the time-independent coupled cluster method for the polarization propagator [R. Moszynski, P. S. Żuchowski, and B. Jeziorski, Coll. Czech. Chem. Commun. {\bf 70}, 1109 (2005)]. Working expressions have been obtained and implemented with the coupled cluster method limited to single, double, and linear triple excitations (CC3). Selected dipole and quadrupole transition probabilities of the alkali earth atoms, computed with the new transition density matrices are compared to the experimental data. Good agreement between theory and experiment is found. The results obtained with the new approach are of the same quality as the results obtained with the linear response coupled cluster theory (LRCC). The one-electron density matrices for the ground state in the CC3 approximation have also been implemented. The dipole moments for a few representative diatomic molecules have been computed with several variants of the new approach, and the results are discussed to choose the approximation with the best balance between the accuracy and computational efficiency.

physics.chem-ph↗

arXiv2014

Approaching exact hyperpolarizabilities via sum-over-states Monte Carlo configuration interaction

We propose using sum-over-states calculations with the compact wavefunctions of Monte Carlo configuration interaction to approach accurate values for higher-order dipole properties up to second hyperpolarizabilities in a controlled way. We apply the approach to small systems that can generally be compared with full configuration interaction (FCI) results. We consider hydrogen fluoride with a 6-31g basis and then look at results, including frequency dependent properties, in an aug-cc-pVDZ basis. We extend one calculation beyond FCI by using an aug-cc-pVTZ basis. The properties of an H$_{4}$ molecule with multireference character are calculated in an aug-cc-pVDZ basis. We then investigate this method on a strongly multireference system with a larger FCI space by modelling the properties of carbon monoxide with a stretched geometry. The behavior of the approach with increasing basis size is considered by calculating results for the neon atom using aug-cc-pVDZ to aug-cc-pVQZ. We finally test if the unusual change in polarizability between the first two states of molecular oxygen can be reproduced by this method in a 6-31g basis.

physics.chem-ph↗

arXiv2014

Energy-dependent resonance broadening in symmetric and asymmetric molecular junctions from an ab initio non-equilibrium Green's function approach

The electronic structure of organic-inorganic interfaces often feature resonances originating from discrete molecular orbitals coupled to continuum lead states. An example are molecular junctions, individual molecules bridging electrodes, where the shape and peak energy of such resonances dictate junction conductance, thermopower, I-V characteristics and related transport properties. In molecular junctions where off-resonance coherent tunneling dominates transport, resonance peaks in the transmission function are often assumed to be Lorentzian functions with an energy-independent broadening parameter $Γ$. Here we define a new energy-dependent resonance broadening function, $Γ(E)$, based on diagonalization of non-Hermitian matrices, which can describe resonances of a more complex, non-Lorentzian nature and can be decomposed into components associated with the left and right lead, respectively. We compute this quantity via an \emph{ab initio} non-equilibrium Green's function approach based on density functional theory for both symmetric and asymmetric molecular junctions, and show that our definition of $Γ(E)$, when combined with Breit-Wigner formula, reproduces the transmission calculated from DFT-NEGF. Through a series of examples, we illustrate how this approach can shed new light on experiments and understanding of junction transport properties in terms of molecular orbitals.

cond-mat.mes-hall↗

arXiv2014

Theory of Triplet Optical Absorption in Oligoacenes: From Naphthalene to Heptacene

In this paper we present a detailed theory of the triplet states of oligoacenes containing up to seven rings, i.e., starting from naphthalene all the way up to heptacene. In particular, we present results on the optical absorption from the first triplet excited state $1^{3}B_{2u}^{+}$ of these oligomers, computed using the Pariser-Parr-Pople (PPP) model Hamiltonian, and a correlated electron approach employing the configuration-interaction (CI) methodology at various levels. Excitation energies of various triplets states obtained by our calculations are in good agreement with the experimental results, where available. The computed triplet spectra of oligoacenes exhibits rich structure dominated by two absorption peaks of high intensities, which are well separated in energy, and are caused by photons polarized along the conjugation direction. This prediction of ours can be tested in future experiments performed on oriented samples of oligoacenes.

physics.chem-ph↗

arXiv2014

Exact Stochastic Unraveling of an Optical Coherence Dynamics by Cumulant Expansion

A numerically exact Monte Carlo scheme for calculation of open quantum system dynamics is proposed and implemented. The method consists of a Monte-Carlo summation of a perturbation expansion in terms of trajectories in Liouville phase-space with respect to the coupling between the excited states of the molecule. The trajectories are weighted by a complex decoherence factor based on the second-order cumulant expansion of the environmental evolution. The method can be used with an arbitrary environment characterized by a general correlation function and arbitrary coupling strength. It is formally exact for harmonic environments, and it can be used with arbitrary temperature. Time evolution of an optically excited Frenkel exciton dimer representing a molecular exciton interacting with a charge transfer state is calculated by the proposed method. We calculate the evolution of the optical coherence elements of the density matrix and linear absorption spectrum, and compare them with the predictions of standard simulation methods.

physics.chem-ph↗

arXiv2014

Quasi-particle energy spectra in local reduced density matrix functional theory

Recently, we introduced (e-print arXiv:1407.7128) {\em local reduced density matrix functional theory} (local RDMFT), a theoretical scheme capable of incorporating static correlation effects in Kohn-Sham equations. Here, we apply local RDMFT to molecular systems of relatively large size, as a demonstration of its computational efficiency and its accuracy in predicting single-electron properties from the eigenvalue spectrum of the single-particle Hamiltonian with a local effective potential. We present encouraging results on the photoelectron spectrum of molecular systems and the relative stability of C$_{20}$ isotopes. In addition, we propose a modelling of the fractional occupancies as functions of the orbital energies that further improves the efficiency of the method useful in applications to large systems and solids.

physics.chem-ph↗

arXiv2014

Direct Experimental Determination of Spectral Densities of Molecular Complexes

Determining the spectral density of a molecular system immersed in a proteomic scaffold and in contact to a solvent is a fundamental challenge in the coarse-grained description of, e.g., electron and energy transfer dynamics. Once the spectral density is characterized, all the time scales are captured and no artificial separation between fast and slow processes need be invoked. Based on the fluorescence Stokes shift function, we utilize a simple and robust strategy to extract the spectral density of a number of molecular complexes from available experimental data. Specifically, we show that experimental data for dye molecules in several solvents, amino acid proteins in water, and some photochemical systems (e.g., rhodopsin and green fluorescence proteins), are well described by a three-parameter family of sub-Ohmic spectral densities that are characterized by a fast initial Gaussian-like decay followed by a slow algebraic-like decay rate at long times.

quant-ph↗

arXiv2014

Vibron transport in macromolecular chains

We study the hopping mechanism of the vibron excitation transport in the simple 1D model of biological macromolecular chains. We supposed that the vibron interaction with thermal oscillations of the macromolecular structural elements will result in vibron self -trapping, and the formation of the partial dressed vibron state. With use of the modified Holstein polaron model, we calculate vibron diffusivity in dependence of the basic system parameters and temperature. We obtain that the vibron diffusivity smoothly decreases in non adiabatic limit when the strength of the vibron-phonon coupling grows. However this dependence becomes by discontinuous one in case of growth of the adiabaticity of the system. The value of the critical point depends of the system temperature, and at room temperatures it belongs to the low or intermediate coupling regime. We discuss an application of these results to study of vibron transport to 3D bundles of such macromolecules chains considering it as polymer nanorods and to 2D polymer films organized from such macromolecules.

cond-mat.mes-hall↗

arXiv2014

Two-phase flow in a chemically active porous medium

We study the problem of the transformation of a given reactant species into an immiscible product species, as they flow through a chemically active porous medium. We derive the equation governing the evolution of the volume fraction of the species -- in a one-dimensional macroscopic description --, identify the relevant dimensionless numbers, and provide simple models for capillary pressure and relative permeabilities, which are quantities of crucial importance when tackling multiphase flows in porous media. We set the domain of validity of our models and discuss the importance of viscous coupling terms in the extended Darcy's law. We investigate numerically the steady regime and demonstrate that the spatial transformation rate of the species along the reactor is non-monotonous, as testified by the existence of an inflection point in the volume fraction profiles. We obtain the scaling of the location of this inflection point with the dimensionless lengths of the problem. Eventually, we provide key elements for optimization of the reactor.

physics.flu-dyn↗

arXiv2014

Testing and Using the Lewin-Lieb Bound in Density Functional Theory

Lewin and Lieb have recently proven several new bounds on the exchange-correlation energy that complement the Lieb-Oxford bound. We test these bounds for atoms, for slowly-varying gases, and for Hooke's atom, finding them usually less strict than the Lieb-Oxford bound. However, we also show that, if a generalized gradient approximation (GGA) is to guarantee satisfaction of the new bounds for all densities, new restrictions on the the exchange-correlation enhancement factor are implied.

physics.chem-ph↗

arXiv2018

Structure-based Sampling and Self-correcting Machine Learning for Accurate Calculations of Potential Energy Surfaces and Vibrational Levels

We present an efficient approach for generating highly accurate molecular potential energy surfaces (PESs) using self-correcting, kernel ridge regression (KRR) based machine learning (ML). We introduce structure-based sampling to automatically assign nuclear configurations from a pre-defined grid to the training and prediction sets, respectively. Accurate high-level \textit{ab initio} energies are required only for the points in the training set, while the energies for the remaining points are provided by the ML model with negligible computational cost. The proposed sampling procedure is shown to be superior to random sampling and also eliminates the need for training several ML models. Self-correcting machine learning has been implemented such that each additional layer corrects errors from the previous layer. The performance of our approach is demonstrated in a case study on a published high-level \textit{ab initio} PES of methyl chloride with 44,819 points. The ML model is trained on sets of different size and then used to predict the energies for tens of thousands of nuclear configurations within seconds. The resulting datasets are utilized in variational calculations of the vibrational energy levels of CH$_3$Cl. By using both structure-based sampling and self-correction, the size of the training set can be kept small (e.g. 10\% of the points) without any significant loss of accuracy. In \textit{ab initio} rovibrational spectroscopy, it is thus possible to reduce the number of computationally costly electronic structure calculations through structure-based sampling and self-correcting KKR-based machine learning by up to 90\%.

physics.chem-ph↗

arXiv2017

Spin-dependent charge recombination along para-phenylene molecular wires

We have used an efficient new quantum mechanical method for radical pair recombination reactions to study the spin-dependent charge recombination along PTZ$^{\bullet+}$--Ph$_n$--PDI$^{\bullet-}$ molecular wires. By comparing our results to the experimental data of E. Weiss {\em et al.} [J. Am. Chem. Soc. {\bf 126}, 5577 (2004)], we are able to extract the spin-dependent (singlet and triplet) charge recombination rate constants for wires with $n=2-5$. These spin-dependent rate constants have not been extracted previously from the experimental data because they require fitting its magnetic field-dependence to the results of quantum spin dynamics simulations. We find that the triplet recombination rate constant decreases exponentially with the length of the wire, consistent with the superexchange mechanism of charge recombination. However, the singlet recombination rate constant is nearly independent of the length of the wire, suggesting that the singlet pathway is dominated by an incoherent hopping mechanism. A simple qualitative explanation for the different behaviours of the two spin-selective charge recombination pathways is provided in terms of Marcus theory. We also find evidence for a magnetic field-independent background contribution to the triplet yield of the charge recombination reaction, and suggest several possible explanations for it. Since none of these explanations is especially compelling given the available experimental evidence, and since the result appears to apply more generally to other molecular wires, we hope that this aspect of our study will stimulate further experimental work.

physics.chem-ph↗

arXiv2019

Gas-phase structural isomer identification by Coulomb explosion of aligned molecules

The gas-phase structures of four difluoroiodobenzene and two dihydroxybromobenzene isomers were identified by correlating the emission angles of atomic fragment ions created following femtosecond laser-induced Coulomb explosion. The structural determinations were facilitated by confining the most polarizable axis of each molecule to the detection plane prior to the Coulomb explosion event using one-dimensional laser-induced adiabatic alignment. For a molecular target consisting of two difluoroiodobenzene isomers, each constituent structure could additionally be singled out and distinguished.

physics.chem-ph↗

arXiv2018

Strong laser alignment of solvent-solute aggregates in the gas-phase

Strong quasi-adiabatic laser alignment of the indole-water-dimer clusters, an amino-acid chromophore bound to a single water molecule through a hydrogen bond, was experimentally realized. The alignment was visualized through ion and electron imaging following strong-field ionization. Molecular-frame photoelectron angular distributions showed a clear suppression of electron yield in the plane of the ionizing laser's polarization, which was analyzed as strong alignment of the molecular cluster with $\left< \cos^2θ_{2D} \right> \ge$ 0.9.

physics.chem-ph↗