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Reversible conversion over multi-million-times in bond types between metavalent and covalent bonds becomes one of the most promising bases for universal memory. As the conversions have been found in metastable states, extended category of crystal structures from stable states via redistribution of vacancies, researches on kinetic behavior of the vacancies are highly on demand. However, they remain lacking due to difficulties with experimental analysis. Herein, the direct observation of the evolution of chemical states of vacancies clarifies the behavior by combining analysis on charge density distribution, electrical conductivity, and crystal structures. Site-switching of vacancies gradually occurs with diverged energy barriers owing to a unique activation code-the accumulation of vacancies triggers spontaneous gliding along atomic planes to relieve electrostatic repulsion. Study on the behavior can be further applied to multi-phase superlattices composed of Sb2Te3 (2D) and GeTe (3D) sublayers, which represent the superior memory performances but their operating mechanisms were still under debates due to their complexity. The site-switching is favorable (suppressed) when Te-Te bonds are formed as physisorption (chemisorption) over the interface between Sb2Te3 (2D) and GeTe (3D) sublayers driven by configurational entropic gain (electrostatic enthalpic loss). Depending on the type of interfaces between sublayers, phases of the superlattices are classified into metastable and stable states, where the conversion could be only achieved in the metastable state. From this comprehensive understanding on the operating mechanism via kinetic behaviors of vacancies and the metastability, further studies towards vacancy engineering are expected in versatile materials., Comment: 32 pages, 4 figures

Density functional simulations of condensed phase water are typically inaccurate, due to the inaccuracies of approximate functionals. A recent breakthrough showed that the SCAN approximation can yield chemical accuracy for pure water in all its phases, but only when its density is corrected. This is a crucial step toward first-principles biosimulations. However, weak dispersion forces are ubiquitous and play a key role in noncovalent interactions among biomolecules, but are not included in the new approach. Moreover, naïve inclusion of dispersion in HF-SCAN ruins its high accuracy for pure water. Here we show that systematic application of the principles of density-corrected DFT yields a functional (HF-r2SCAN-DC4) which recovers and not only improves over HF-SCAN for pure water, but also captures vital noncovalent interactions in biomolecules, making it suitable for simulations of solutions.

Despite the successful debut of gold nanoclusters (Au NCs) in solar cell applications, Au NCs, compared to dyes and quantum dots, have several drawbacks, such as lower extinction coefficients. Any modulation of the physical properties of NCs can have a significant influence on the delicate control of absorbance, energy levels, and charge separation, which are essential to ensure high power conversion efficiency. To this end, we systematically alter the optoelectronic structure of Au18(SR)14 by Ag doping and explain its influence on solar cell performance. Our in-depth spectroscopic and electrochemical characterization combined with computational study reveals that the performance-dictating factors respond in different manners to the Ag doping level, and we determine that the best compromise is the incorporation of a single Ag atom into an Au NC. This new insight highlights the unique aspect of NCs—susceptibility to atomic level doping—and helps establish a new design principle for efficient NC-based solar cells.

Density functional theory (DFT) calculations have become widespread in both chemistry and materials, because they usually provide useful accuracy at much lower computational cost than wavefunction-based methods. All practical DFT calculations require an approximation to the unknown exchange-correlation energy, which is then used self-consistently in the Kohn-Sham scheme to produce an approximate energy from an approximate density. Density-corrected DFT is simply the study of the relative contributions to the total energy error. In the vast majority of DFT calculations, the error due to the approximate density is negligible. But with certain classes of functionals applied to certain classes of problems, the density error is sufficiently large as to contribute to the energy noticeably, and its removal leads to much better results. These problems include reaction barriers, torsional barriers involving I -conjugation, halogen bonds, radicals and anions, most stretched bonds, etc. In all such cases, use of a more accurate density significantly improves performance, and often the simple expedient of using the Hartree-Fock density is enough. This Perspective explains what DC-DFT is, where it is likely to improve results, and how DC-DFT can produce more accurate functionals. We also outline challenges and prospects for the field.

A Kohn-Sham (KS) inversion determines a KS potential and orbitals corresponding to a given electron density, a procedure that has applications in developing and evaluating functionals used in density functional theory. Despite the utility of KS inversions, application of these methods among the research community is disproportionately small. We implement the KS inversion methods of Zhao-Morrison-Parr and Wu-Yang in a framework that simplifies analysis and conversion of the resulting potential in real-space. Fully documented Python scripts integrate with PySCF, a popular electronic structure prediction software, and Fortran alternatives are provided for computational hot spots., 13 pages, 4 figures, 11 blocks of code

As a 3D topological insulator, bismuth selenide (Bi2Se3) has potential applications for electrically and optically controllable magnetic and optoelectronic devices. Understanding the coupling with its topological phase requires studying the interactions of carriers with the lattice on time scales down to the subpicosecond regime. Here, we investigate the ultrafast carrier-induced lattice contractions and interlayer modulations in Bi2Se3 thin films by time-resolved diffraction using an X-ray free-electron laser. The lattice contraction depends on the carrier concentration and is followed by an interlayer expansion accompanied by oscillations. Using density functional theory and the Lifshitz model, the initial contraction can be explained by van der Waals force modulation of the confined free carrier layers. Our theoretical calculations suggest that the band inversion, related to a topological phase transition, is modulated by the expansion of the interlayer distance. These results provide insights into the topological phase control by light-induced structural change on ultrafast time scales.

Most torsional barriers are predicted to high accuracy (about 1kJ/mol) by standard semilocal functionals, but a small subset has been found to have much larger errors. We create a database of almost 300 carbon-carbon torsional barriers, including 12 poorly behaved barriers, all stemming from Y=C-X group, where X is O or S, and Y is a halide. Functionals with enhanced exchange mixing (about 50%) work well for all barriers. We find that poor actors have delocalization errors caused by hyperconjugation. These problematic calculations are density sensitive (i.e., DFT predictions change noticeably with the density), and using HF densities (HF-DFT) fixes these issues. For example, conventional B3LYP performs as accurately as exchange-enhanced functionals if the HF density is used. For long-chain conjugated molecules, HF-DFT can be much better than exchange-enhanced functionals. We suggest that HF-PBE0 has the best overall performance., Comment: 13 pages, 7 main figures, 6 supporting figures

HF-DFT, the practice of evaluating approximate density functionals on Hartree-Fock densities, has long been used in testing density functional approximations. Density-corrected DFT (DC-DFT) is a general theoretical framework for identifying failures of density functional approximations by separating errors in a functional from errors in its self-consistent (SC) density. Most modern DFT calculations yield highly accurate densities, but important characteristic classes of calculation have large density-driven errors, including reaction barrier heights, electron affinities, radicals and anions in solution, dissociation of heterodimers, and even some torsional barriers. Here, the HF density (if not spin-contaminated) usually yields more accurate and consistent energies than those of the SC density. We use the term DC(HF)-DFT to indicate DC-DFT using HF densities only in such cases. A recent comprehensive study (J. Chem. Theory Comput. 2021, 17, 1368-1379) of HF-DFT led to many unfavorable conclusions. A reanalysis using DC-DFT shows that DC(HF)-DFT substantially improves DFT results precisely when SC densities are flawed.

Kohn-Sham (KS) inversion, that is, the finding of the exact KS potential for a given density, is difficult in localized basis sets. We study the precision and reliability of several inversion schemes, finding estimates of density-driven errors at a useful level of accuracy. In typical cases of substantial density-driven errors, Hartree-Fock density functional theory (HF-DFT) is almost as accurate as DFT evaluated on CCSD(T) densities. A simple approximation in practical HF-DFT also makes errors much smaller than the density-driven errors being calculated. Two paradigm examples, stretched NaCl and the HO·Cl- radical, illustrate just how accurate HF-DFT is.

Empirical fitting of parameters in approximate density functionals is common. Such fits conflate errors in the self-consistent density with errors in the energy functional, but density-corrected DFT (DC-DFT) separates these two. We illustrate with catastrophic failures of a toy functional applied to $H_2^+$ at varying bond lengths, where the standard fitting procedure misses the exact functional; Grimme's D3 fit to noncovalent interactions, which can be contaminated by large density errors such as in the WATER27 and B30 datasets; and double-hybrids trained on self-consistent densities, which can perform poorly on systems with density-driven errors. In these cases, more accurate results are found at no additional cost, by using Hartree-Fock (HF) densities instead of self-consistent densities. For binding energies of small water clusters, errors are greatly reduced. Range-separated hybrids with 100\% HF at large distances suffer much less from this effect.

We have investigated conformational structures of meso- meso linked porphyrin arrays (Z n) by single molecule fluorescence spectroscopy. Modulation depths ( M values) were measured by excitation polarization fluorescence spectroscopy. The M value decreases from 0.85 to 0.46 as the number of porphyrin units increases from 3 to 128, indicating that longer arrays exhibit coiled structures. Such conformational changes depending on the length have been confirmed by coarse-grained simulation. The histograms of M values and traces of centroid position of emitting sites by localization microscopy showed that the structures of longer arrays changed to more stretched after solvent vapor annealing with tetrahydrofuran.

All-electron fixed-node diffusion Monte Carlo provides benchmark spin gaps for four Fe(II) octahedral complexes. Standard quantum chemical methods (semilocal DFT and CCSD(T)) fail badly for the energy difference between their high- and low-spin states. Density-corrected DFT is both significantly more accurate and reliable and yields a consistent prediction for the Fe-Porphyrin complex.

We review the role of self-consistency in density functional theory. We apply a recent analysis to both Kohn-Sham and orbital-free DFT, as well as to Partition-DFT, which generalizes all aspects of standard DFT. In each case, the analysis distinguishes between errors in approximate functionals versus errors in the self-consistent density. This yields insights into the origins of many errors in DFT calculations, especially those often attributed to self-interaction or delocalization error. In many classes of problems, errors can be substantially reduced by using `better' densities. We review the history of these approaches, many of their applications, and give simple pedagogical examples., Comment: submitted for publication to the Annual Review of Physical Chemistry

Density-corrected density functional theory (DC-DFT) is enjoying substantial success in improving semilocal DFT calculations in a wide variety of chemical problems. This paper provides the formal theoretical framework and assumptions for the analysis of any functional minimization with an approximate functional. We generalize DC-DFT to allow comparison of any two functionals, not just comparison with the exact functional. We introduce a linear interpolation between any two approximations, and use the results to analyze global hybrid density functionals. We define the basins of density-space in which this analysis should apply, and give quantitative criteria for when DC-DFT should apply. We also discuss the effects of strong correlation on density-driven error, utilizing the restricted HF Hubbard dimer as an illustrative example., 14 pages, 9 figures

We explore heat transfer and thermal characteristics of a wire-grid polarizer (WGP) on a microscale by investigating the effect of various geometrical parameters such as wire-grid period, height, and a fill factor. The thermal properties arise from heat transfer by light absorption and conduction in wire-grids. Fill factor was found to be the most dominant geometrical parameter. For TM polarized light, a higher fill factor with thicker wire-grids increased the temperature. The local temperature was found to rise up to Tmax = 354.5 K. TE polarization tended to produce lower temperature. Thermal extinction due to polarimetric extinction by a WGP was also evaluated and highest extinction was observed to be 4.78 dB, which represents a temperature difference ΔT = 54.3 °C. We expect the results to be useful for WGPs in polarization-sensitive thermal switching applications.

We argue that any general mathematical measure of density error, no matter how reasonable, is too arbitrary to be of universal use. However, the energy functional itself provides a universal relevant measure of density errors. For the self-consistent density of any Kohn-Sham calculation with an approximate functional, the theory of density-corrected density functional theory (DC-DFT) provides an accurate, practical estimate of this ideal measure. We show how to estimate the significance of the density-driven error even when exact densities are unavailable. In cases with large density errors, the amount of exchange-mixing is often adjusted, but we show that this is unnecessary. Many chemically relevant examples are given.

In this presentation, optical molecular detection techniques based on light localization are explored for optofluidic applications. For improved sensor characteristics in surface plasmon resonance (SPR) detection, surface-enhanced nanoarray structures have been investigated to create locally amplified electromagnetic near-fields on metallic substrates. Surface-enhanced plasmonic nanoarrays structures can create locally amplified electromagnetic near-fields as a consequence of evanescent field localization on metallic substrates. While the effect of light localization in the near-field using plasmonic nanoarrays may be moderate, the approach can be powerful when localized light fields are spatially colocalized with target molecular distribution. As such, various approaches to produce field matter colocalization for applications in detecting molecular interactions are to be discussed, for example, by oblique evaporation-based device fabrication and plasmonic lithography [1-5]. On the other hand, colocalization can be extended on a broader scale to general biomolecular detection beyond SPR and applied to microscopy and imaging. The creation of localized fields has been investigated in many studies in the past because of the potential to improve resolving power for imaging molecular processes typically impossible to observe under diffraction limit. Although emerging approaches have been extremely successful to produce super-resolved images, we explore alternative techniques based on plasmonic nanoarrays by which achievable resolution may be customized to fit the specific imaging needs and at the same time a conventional optical system may be used. Feasibility studies performed on visualizing internalization of virus particles [6], sliding microtubules and bacterial motility on random and periodic nanopatterns will be discussed [7-11]. Enhancement of axial resolution for the detection of intracellular protein distribution is also reported by extraordinary light transmission using graded plasmonic nanoapertures. It is also imperative to understand the force acting on molecules under detection for sensor and imaging applications. Figure 1a-c shows the gradient force produced by a plasmonic nanopost of diameter f = 100, 150, and 200 nm (height: 30 nm, gap between posts: 100 nm, and period: 750 nm) and clearly confirms the trapping force exerted at the post rim. Spectra of electric near-field maximum are also presented in Figure 1d (at the wavelength at which a maximum field strength is obtained for each nanopost, the gradient force in Fig. 1a-c was calculated). The results suggest the possibility of wavelength-dependent switching of the trapping force. This is only one of many application examples of the trapping force that can be applied and has thus been pursued in various optofluidic systems.

We explore plasmon-enhanced wire-gird polarizers (WGPs) to achieve improved polarimetric performance with more relaxed fabrication parameters compared to conventional WGP. A WGP designed with a blazed wire-grid profile was considered for plasmonic enhancement. The results show that a blazed WGP can achieve extremely high polarimetric extinction at a longer wire-grid period (Lambda) compared to conventional WGP structure. Under the optimum geometrical parameters, a blazed WGP may attain an extinction ratio of over 40 dB at Lambda = 800 nm, which may allow photolithography for fabrication. In contrast, conventional WGPs obtained comparable performance at Lambda = 200 nm, requiring more difficult lithographic techniques. The study can therefore be of significant importance for WGPs to be more widely available for diverse applications. (C) 2017 Optical Society of America

Density-corrected DFT is a method that cures several failures of self-consistent semilocal DFT calculations by using a more accurate density instead. A novel procedure employs the Hartree-Fock density to bonds that are more severely stretched than ever before. This substantially increases the range of accurate potential energy surfaces obtainable from semilocal DFT for many heteronuclear molecules. We show that this works for both neutral and charged molecules. We explain why and explore more difficult cases, for example, CH(+), where density-corrected DFT results are even better than sophisticated methods like CCSD. We give a simple criterion for when DC-DFT should be more accurate than self-consistent DFT that can be applied for most cases.

We model lattice-mismatched group III-V semiconductor InxGa1-xAs alloys with the three-parameter anharmonic Kirkwood-Keating potential, which includes realistic distortion effect by introducing anharmonicity. Although the potential parameters were determined based on optical properties of the binary parent alloys InAs and GaAs, simulated dielectric functions, reflectance, and Raman spectra of alloys agree excellently with experimental data for any arbitrary atomic composition. For a wide range of atomic composition, InAs- and GaAs-bond retain their respective properties of binary parent crystals despite lattice and charge mismatch. It implies that use of the anharmonic Kirkwood-Keating potential may provide an optimal model system to investigate diverse and unique optical properties of quantum dot heterostructures by circumventing potential parameter searches for particular local structures.

We investigated the excitation energy transfer process of meso-meso linked zinc(II) porphyrin arrays using the on-the-fly filtered propagator path integral method. Details of the dynamics such as coherence length of a porphyrin array are estimated by analysis of the characteristics of forward-backward pair trajectories. Upon examination of the convergence of the reduced density matrix with respect to the subset of Hilbert space trajectories, we determine the number of porphyrin units that form collective coherent states, that is, the coherence length. Simulation results show that the coherence length of zinc(II) porphyrin arrays is up to 4 units, which agrees excellently with experimental observations. On the other hand, the energy bias provided by the energy-accepting 5,15-bisphenylethynylated zinc(II) porphyrin reduces the degree of coherence which becomes negligible for an array with more than for porphyrin units. Considering conformational inhomogeneity, we found that the experimentally determined coherence length is the result of electronic and environmental influence rather than the structure disorder. Temperature dependence is also discussed.

We explore distance dependent variation of the coherence length relevant to DNA charge-transfer processes within 5'-GAnG3-3' DNA sequences. Recently developed on-the-fly filtered propagator functional path integral approach was employed to sort out transport trajectories with significant contribution and to analyze correlation between electronic states. In particular, the coherence length was quantitatively determined through characteristics of off-diagonal quantum trajectories. Simulated coherence lengths and experimentally observed rate constants [Nature 2001, 412, 318] were found to be consistent such that, up to n = 2, the exponential decrease of the rate constants is associated with the donor-acceptor coherence driven charge transfer. In contrast, the rate constants become insensitive to the distance for nor = 3 in which donor and acceptor are no longer significantly correlated. It was also found that the coherence within a collective state governs the overall charge transfer, which is composed of a part of a sequence within the coherence length from the donor.

With the density matrix decomposition scheme of the path integral method, an accurate quantitative analysis on bridge-mediated pathways in long-range charge transfer processes is presented. Unlike a donor-bridge-acceptor triad, a long-range charge transfer process with a number of bridges has additional pathways in which charges always migrate through bridges but not necessarily by incoherent nearest-neighbor hopping. By employing the density matrix decomposition and sorting the incoherent nearest-neighbor and the coherent next-nearest-neighbor hopping pathways, respective contributions to the charge transfer are evaluated quantitatively. Numerical results of two series of configurations with varying degrees of coherence within the system have found that, depending on the configuration, the contribution of the coherent pathways other than superexchange pathways is significant. In the presence of the coherence, long-range charge transfer dynamics may be dominated by the through-bridge mechanism that consists of the coherent through-bridge pathways as well as the incoherent nearest-neighbor hopping pathways.

Time evolution of the charge-transfer site population is studied in a short DNA sequence to determine the type of governing charge-transfer mechanism. The system consists of a 5'-GAGGG-3' nucleobase sequence coupled with a dissipative bath that represents the DNA phosphate backbone and solvents. Relative contribution of transfer mechanisms to the whole charge-transfer process has been obtained using the on-the-fly filtered propagator functional path integral method with the density matrix decomposition. Partial density matrixes of the incoherent hopping and coherent superexchange pathways as well as the full reduced density matrix have been evaluated and discussed for both debye and ohmic baths. It was found that the relative contribution of the transfer mechanisms is rather sensitive to the frequency-dependent environmental description.

We have investigated the overall excitation energy relaxation dynamics in linear porphyrin arrays as well as the energy transport phenomena by attaching an energy acceptor to one end of a linear porphyrin array by using steady state and time-resolved spectroscopic measurements. We have revealed that the solvation dynamics as well as the conformational dynamics contributes significantly to the energy relaxation processes of linear porphyrin arrays. Consequently, long porphyrin arrays no longer serve as good energy transmission elements in donor-acceptor linked systems due to conformational heterogeneities which provide the non-radiative deactivation channels as energy quenchers.

In this paper we develop a “diatomic in molecules semiempirical ligand field” (DIMSELF) method to calculate ground and excited many-body potential energy surfaces for an arbitrary transition metal ion in an arbitrary complex system. This method is not restricted to a high-symmetry environment and is meant to be inexpensive and suitable for nonadiabatic excited states dynamics on-the-fly. Within the approximations employed, the method includes full CI (configuration interaction) and SO (spin-orbit) interactions, essential to the description of nonradiative transitions such as those of myoglobin in the presence of carbon monoxide. We test our method against high level ab initio calculations for a simple model system of myoglobin’s heme pocket. Finally, we discuss our results and compare with previous calculations in the literature. Transition metal complexes play a fundamental role in many technological and biological areas. They act as catalysts in the oil industry during the processes of cracking and reforming, they are also fundamental for oxygen transport in blood, and they are key to plant respiration. Some of these processes can be well understood without the need to include the small contribution of spin-orbit (SO) interaction which, for the most part, is of the order of the error one performs in ab initio calculations of these kind of systems. In some cases, however, nonradiative transitions occur between states with different spins. Of particular interest are heme proteins, a biologically important group of molecules that have a unique common active site: an iron-protoporphyrin-IX complex, where changes in spin state can be an integral part of the protein function. One of the most striking biological manifestations of this modulation is the binding of molecular oxygen and carbon monoxide (CO) 1-9 to the five-coordinated ferrous heme site of globins. Another wellstudied example is the situation of several spin changes in the enzymatic activation cycles of cytochromes P450. These transitions are solely due to SO coupling and are otherwise forbidden. Ab initio calculations are performed within the framework of Hund’s Case A and hence assume that S, the total spin of the system, is a good quantum number. Spin-orbit coupling matrix elements could then be added, and rediagonalization of the Hamiltonian matrix would provide us with the spin coupled eigenstates of the system. Obtaining several electronic excited states for a given spin multiplicity is complex, and for mediumsized systems only configuration interaction for single excitations (CIS) is affordable. However, a more complete description of excited states might be required for the study of dynamics. For large systems, where the environment can be introduced by mixing quantum chemistry with molecular mechanics, electronically excited states are rarely computationally accessible and only the fundamental ground state for each spin multiplicity might be computed. For nonsymmetric systems, even at the density functional theory (DFT) level of theory, several attempts with different initial guesses should be considered in order to achieve the true ground state. The computational effort is drastically increased when several nuclear configurations are required for a complete study of the dynamics, and calculations on-the-fly, including excited states and SO coupling, are simply out of the question. Therefore, a semiempirical approach that includes excited states and SO coupling is very desirable. The method we develop in this paper is a generalization of Gerloch’s 10 cellular AOM (angular overlap model) version of ligand field theory, combined with a semiempirical version of Ellison’s 11-13 DIM (diatomics in molecules). Neither ligand field theory nor the semiempirical version of DIM are exact ab initio methods; not all the parameters can be obtained by analytical methods and they ought to be fitted either to experimental data or other calculations. On the other hand, once these parameters are known, fast computation of ground- and excited-state potentials can be performed without having to recalculate wave functions and their matrix elements. We test this method against a simplified model of the heme

Standard density functional approximations often give questionable results for odd-electron radical complexes, with the error typically attributed to self-interaction. In density corrected density functional theory (DC-DFT), certain classes of density functional theory calculations are significantly improved by using densities more accurate than the self-consistent densities. We discuss how to identify such cases, and how DC-DFT applies more generally. To illustrate, we calculate potential energy surfaces of HO·Cl-and HO·H2O complexes using various common approximate functionals, with and without this density correction. Commonly used approximations yield wrongly shaped surfaces and/or incorrect minima when calculated self consistently, while yielding almost identical shapes and minima when density corrected. This improvement is retained even in the presence of implicit solvent. © 2014 AIP Publishing LLC.

A method for calculating the quantum canonical rate constant of chemical reactions in a many body system by means of a short-time flux autocorrelation function combined with a maximum entropy numerical analytic continuation scheme is presented. The rate constant is expressed as the time integral of the real-time flux autocorrelation function. The real-time flux autocorrelation function is evaluated for short times fully quantum mechanically by path integral Monte Carlo simulations. The maximum entropy approach is then used to extract the rate from the short real-time flux autocorrelation data. We present two numerical tests, one for proton transfer in harmonic dissipative environments in the deep tunneling regime and the other for the two-level model of primary charge separation in the photosynthetic reaction center. The results obtained using the flux autocorrelation data up to the time of no more than βℏ are in excellent agreement with the exact quantum calculation over a wide range of parameters includ...

We present accurate path integral simulations of the primary charge separation in bacterial photosynthesis. The process is modeled in terms of the three coupled electronic states corresponding to the photoexcited special pair (the electron donor), the reduced accessory bacteriochlorophyll (the bridge), and the reduced bacteriopheophytin (the primary electron acceptor) of the L branch which interact with a dissipative medium of protein and solvent degrees of freedom. The electronic state populations are followed over 17 ps via an iterative procedure that employs a propagator functional [Comput. Phys. Commun. 1997, 99, 335]. In a previous article [Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 3926] the free energy of the reduced accessory bacteriochlorophyll state and its coupling to the excited special pair were estimated by comparing the simulation results against available experimental observations on wild-type and modified reaction centers. The determined optimal parameters correspond to a simple two-step ele...

We decompose the energy error of any variational density functional theory calculation into a contribution due to the approximate functional and that due to the approximate density. Typically, the functional error dominates, but in many interesting situations the density-driven error dominates. Examples range from calculations of electron affinities to preferred geometries of ions and radicals in solution. In these abnormal cases, the error in density functional theory can be greatly reduced by using a more accurate density. A small orbital gap often indicates a substantial density-driven error. © 2013 American Physical Society.

We introduce frustrated aggregate internal rearrangement (FAIR) mechanism for anisotropic higher-order structure formations, in which the anisotropy arose due to the structural frustration. We demonstrate the FAIR mechanism by investigating the recently observed rigid organic nanotube formations through the self-assembly of building blocks, which include rigid segments and make intermolecular H-bonds, whereas the principle of the FAIR mechanism is general and is not limited to H-bonding building blocks or nanotube formations. Initially, molecules aggregate into sheetlike structures driven by nonspecific and nondirectional intermolecular interactions such as π-π stacking or amphiphilicity. Weak intermolecular H-bonds provide additional stability to the structure. Within the aggregate, however, not all molecules have the right orientation for specific and directional H-bonds whereas collective internal rearrangement of rigid building blocks requires a large amount of energy to overcome kinetically trapped barriers. Consequently, instead of the fully H-bonded global equilibrium structure, self-assembled layers become trapped with partial and disordered H-bonding schemes at various fractions leading to an anisotropic layer that undergoes spontaneous transformation into curved structures. The FAIR mechanism can readily be extended to anisotropic higher-order structures other than nanotubes and to the assembly of diverse building blocks including hybrids such as polymer nanocomposites. Also the reversible transformation from metastable nanotubes into layered sheets is potentially useful for controlling internal cavity size of nanotubes.

Accurate quantum mechanical simulations of the primary charge transfer in photosynthetic reaction centers are reported. The process is modeled by three coupled electronic states corresponding to the photoexcited chlorophyll special pair (donor), the reduced bacteriopheophytin (acceptor), and the reduced accessory chlorophyll (bridge) that interact with a dissipative medium of protein and solvent degrees of freedom. The time evolution of the excited special pair is followed over 17 ps by using a fully quantum mechanical path integral scheme. We find that a free energy of the reduced accessory chlorophyll state approximately equal to 400 cm(-1) lower than that of the excited special pair state yields state populations in agreement with experimental results on wild-type and modified reaction centers. For this energetic configuration electron transfer is a two-step process.

We present a modified Feynman and Vernon's path integral formalism which allows independent consideration of coherent superexchange and incoherent hopping pathways of charge transfer processes in order to determine the type of transport mechanism. By classifying the pathways between donor and acceptor into different mechanisms and by decomposing the density matrix of donor-bridge-acceptor triads into corresponding partial matrices, the contribution of each mechanism is obtained separately. Numerical tests confirm that the scheme is valid and efficient in exploring the transport mechanism and that the incoherent hopping mechanism tends to govern charge transfer processes even in systems with high-energy bridge states.

Using dissipative particle dynamics, we inves- tigated the graft configuration-dependent scroll formation of sheet polymers and their morphologies. Two types of coarse- grained graft disorder models were considered at various displaced tether fractions. Although tether coils were identical, sheet anisotropy arose from discrepancies in graft config- urations on the two opposite-side surfaces and resulted in spontaneous scroll formation. An anisotropy parameter based on the relative free volumes of tether coils was introduced and shown to be linearly related to the radius of gyration. This demonstrates that sheet anisotropy, and consequently internal cavity diameters of tubular scrolls, can be regulated by surface grafting. We also examined a coassembly of laterally grafted rod−coil amphiphiles as an alternative way to form sheet polymers with heterosurfaces. The coassembly of conformation mismatching rod−coil molecules is expected to form anisotropic bilayers, as each layer is assembled independently with different degrees of graft disorder. We believe this work provides a framework for further research regarding morphology control by surface grafts of sheet polymers.

We employ a Monte Carlo (MC) algorithm to investigate the decoherence of diffuse photons in turbid media. For the MC simulation of coherent photons, the degree of coherence, defined as a random variable for a photon packet, is associated with a decoherence function that depends on the scattering angle and is updated as a photon interacts with a medium via scattering. Using a slab model, the effects of medium scattering properties were studied, which reveals that a linear random variable model for the degree of coherence is in better agreement with experimental results than a sinusoidal model and that decoherence is quick for the initial few scattering events followed by a slow and gradual decrease of coherence.