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arXiv2013

Atomistic study of energy funneling in the light-harvesting complex of green sulfur bacteria

Phototrophic organisms such as plants, photosynthetic bacteria and algae use microscopic complexes of pigment molecules to absorb sunlight. Within the light-harvesting complexes, which frequently have several functional and structural subunits, the energy is transferred in the form of molecular excitations with very high efficiency. Green sulfur bacteria are considered to be amongst the most efficient light-harvesting organisms. Despite multiple experimental and theoretical studies of these bacteria the physical origin of the efficient and robust energy transfer in their light-harvesting complexes is not well understood. To study excitation dynamics at the systems level we introduce an atomistic model that mimics a complete light-harvesting apparatus of green sulfur bacteria. The model contains approximately 4000 pigment molecules and comprises a double wall roll for the chlorosome, a baseplate and six Fenna-Matthews-Olson trimer complexes. We show that the fast relaxation within functional subunits combined with the transfer between collective excited states of pigments can result in robust energy funneling. Energy transfer is robust on the initial excitation conditions and temperature changes. Moreover, the same mechanism describes the coexistence of multiple timescales of excitation dynamics frequently observed in ultrafast optical experiments. While our findings support the hypothesis of supertransfer, the model reveals energy transport through multiple channels on different length scales.

physics.chem-ph↗

arXiv2014

Hydrogen Ordering and New Polymorph of Layered Perovskite Oxyhydrides: Sr2VO4-xHx

Compositionally tunable vanadium oxyhydrides Sr2VO4-xHx (x = 0 - 1) without considerable anion vacancy were synthesized by high-pressure solid state reaction. The crystal structures and their properties were characterized by powder neutron diffraction, synchrotron X-ray diffraction, thermal desorption spectroscopy, and first-principles density functional theory (DFT) calculations. The hydrogen anions selectively replaced equatorial oxygen sites in the VO6 layers via statistical substitution of hydrogen in the low x region (x < 0.2). A new orthorhombic phase (Immm) with an almost entirely hydrogen-ordered structure formed from the K2NiF4-type tetragonal phase with x > 0.7. Based on the DFT calculations, the degree of oxygen/hydrogen anion ordering is strongly correlated with the bonding interaction between vanadium and the ligands.

cond-mat.mtrl-sci↗

arXiv2014

Role of Pyridine as a Biomimetic Organo-Hydride for Homogeneous Reduction of CO2 to Methanol

We use quantum chemical calculations to elucidate a viable homogeneous mechanism for pyridine-catalyzed reduction of CO2 to methanol. In the first component of the catalytic cycle, pyridine (Py) undergoes a H+ transfer (PT) to form pyridinium (PyH+) followed by an e- transfer (ET) to produce pyridinium radical (PyH0). Examples of systems to effect this ET to populate the LUMO of PyH+(E0calc ~ -1.3V vs. SCE) to form the solution phase PyH0 via highly reducing electrons include the photo-electrochemical p-GaP system (ECBM ~ -1.5V vs. SCE at pH= 5) and the photochemical [Ru(phen)3]2+/ascorbate system. We predict that PyH0 undergoes further PT-ET steps to form the key closed-shell, dearomatized 1,2-dihydropyridine (PyH2) species. Our proposed sequential PT-ET-PT-ET mechanism transforming Py into PyH2 is consistent with the mechanism described in the formation of related dihydropyridines. Because it is driven by its proclivity to regain aromaticity, PyH2 is a potent recyclable organo-hydride donor that mimics the role of NADPH in the formation of C-H bonds in the photosynthetic CO2 reduction process. In particular, in the second component of the catalytic cycle, we predict that the PyH2/Py redox couple is kinetically and thermodynamically competent in catalytically effecting hydride and proton transfers (the latter often mediated by a proton relay chain) to CO2 and its two succeeding intermediates, namely formic acid and formaldehyde, to ultimately form CH3OH. The hydride and proton transfers for the first reduction step, i.e. reduction of CO2, are sequential in nature; by contrast, they are coupled in each of the two subsequent hydride and proton transfers to reduce formic acid and formaldehyde.

physics.chem-ph↗

arXiv2018

Windowless Observation of Evaporation-Induced Coarsening of Au-Pt Nanoparticles in Polymer Nanoreactors

The interactions between nanoparticles and solvents play a critical role in the formation of complex, metastable nanostructures. However, direct observation of such interactions with high spatial and temporal resolution is challenging with conventional liquid-cell transmission electron microscopy (TEM) experiments. Here, a windowless system consisting of polymer nanoreactors deposited via scanning probe block copolymer lithography (SPBCL) on an amorphous carbon film is used to investigate the coarsening of ultrafine (1-3 nm) Au-Pt bimetallic nanoparticles as a function of solvent evaporation. In such reactors, homogeneous Au-Pt nanoparticles are synthesized from metal ion precursors in situ under electron irradiation. The non-uniform evaporation of the thin polymer film not only concentrates the nanoparticles, but also accelerates the coalescence kinetics at the receding polymer edges. Qualitative analysis of the particle forces influencing coalescence suggests that capillary dragging by the polymer edges plays a significant role in accelerating this process. Taken together, this work: 1) provides fundamental insight into the role of solvents in the chemistry and coarsening behavior of nanoparticles during the synthesis of polyelemental nanostructures, 2) provides insight into how particles form via the SPBCL process, and 3) shows how SPBCL-generated domes, instead of liquid cells, can be used to study nanoparticle formation. More generally, it shows why conventional models of particle coarsening, which do not take into account solvent evaporation, cannot be used to describe what is occurring in thin film, liquid-based syntheses of nanostructures.

physics.chem-ph↗

arXiv2019

Elucidating the NuclearQuantum Dynamics of Intramolecular Double Hydrogen Transfer in Porphycene

We address the double hydrogen transfer (DHT) dynamics of the porphycene molecule: A complex paradigmatic system where the making and breaking of H-bonds in a highly anharmonic potential energy surface requires a quantum mechanical treatment not only of the electrons, but also of the nuclei. We combine density-functional theory calculations, employing hybrid functionals and van der Waals corrections, with recently proposed and optimized path-integral ring-polymer methods for the approximation of quantum vibrational spectra and reaction rates. Our full-dimensional ring-polymer instanton simulations show that below 100 K the concerted DHT tunneling pathway dominates, but between 100 K and 300 K there is a competition between concerted and stepwise pathways when nuclear quantum effects are included. We obtain ground-state reaction rates of $2.19 \times 10^{11} \mathrm{s}^{-1}$ at 150 K and $0.63 \times 10^{11} \mathrm{s}^{-1}$ at 100 K, in good agreement with experiment. We also reproduce the puzzling N-H stretching band of porphycene with very good accuracy from thermostatted ring-polymer molecular dynamics simulations. The position and lineshape of this peak, centered at around 2600 cm$^{-1}$ and spanning 750 cm$^{-1}$, stems from a combination of very strong H-bonds, the coupling to low-frequency modes, and the access to $cis$-like isomeric conformations, which cannot be appropriately captured with classical-nuclei dynamics. These results verify the appropriateness of our general theoretical approach and provide a framework for a deeper physical understanding of hydrogen transfer dynamics in complex systems.

physics.chem-ph↗

arXiv2014

Microcalorimetric and SAXS Determination of PEO-SDS Interactions: The Effect of Cosolutes Formed by Ions

The effect of different ionic cosolutes (NaCl, Na$_2$SO$_4$, Li$_2$SO$_4$, NaSCN, Na$_2$[Fe(CN)5NO], and Na$_3$[Co(NO)$_6$]) on the interaction between sodium dodecyl sulfate (SDS) and poly(ethylene oxide) (PEO) was examined by small-angle X-ray scattering (SAXS) and isothermal titration calorimetric techniques. The critical aggregation concentration values (cac), the saturation concentration ($C_2$), the integral enthalpy change for aggregate formation ($ΔH_{\mbox{agg}}$(int)) and the standard free energy change of micelle adsorption on the macromolecule chain ( $ΔΔG_{\mbox{agg}}$) were derived from the calorimetric titration curves. In the presence of 1.00 mmol L$^{-1}$ cosolute, no changes in the parameters were observed when compared with those obtained for SDS-PEO interactions in pure water. For NaCl, Na$_2$SO$_4$, Li$_2$SO$_4$, and NaSCN at 10.0 and 100 mmol L$^{-1}$, the cosolute presence lowered cac, increased $C_2$, and the PEO-SDS aggregate became more stable. In the presence of Na$_2$[Fe(CN)5NO], the calorimetric titration curves changed drastically, showing a possible reduction in the PEO-SDS degree of interaction, possibility disrupting the formed nanostructure; however, the SAXS data confirmed, independent of the small energy observed, the presence of aggregates adsorbed on the polymer chain.

cond-mat.mtrl-sci↗

arXiv2013

Ice Formation via Deposition Mode Nucleation on Bare and Alcohol-covered Graphite Surfaces

Deposition of water on aerosol particles contributes to ice cloud formation in the atmosphere with implications for the water cycle and climate on Earth. The heterogeneous ice nucleation process is influenced by physico-chemical properties of the substrate, but the mechanisms remain incompletely understood. Here, we report on ice formation on bare and alcohol-covered graphite at temperatures from 175 to 213 K, probed by elastic helium and light scattering. Water has a low wettability on bare and butanol-covered graphite resulting in the growth of rough ice surfaces. In contrast, pre-adsorbed methanol provides hydrophilic surface sites and results in the formation of smooth crystalline ice; an effect that is pronounced also for sub-monolayer methanol coverages. The alcohols primarily reside at the ice surface and at the ice-graphite interface with a minor fraction being incorporated into the growing ice structures. Methanol has no observable effect on gas/solid water vapor exchange whereas butanol acts as a transport barrier for water resulting in a reduction in ice evaporation rate at 185 K. Implications for the description of deposition mode freezing are discussed.

physics.chem-ph↗

arXiv2013

Surface Transformations and Water Uptake on Liquid and Solid Butanol near the Melting Temperature

Water interactions with organic surfaces are of central importance in biological systems and many Earth system processes. Here we describe experimental studies of water collisions and uptake kinetics on liquid and solid butanol from 160 to 200 K. Hyperthermal D2O molecules (0.32 eV) undergo efficient trapping on both solid and liquid butanol, and only a minor fraction scatters inelastically after an 80% loss of kinetic energy to surface modes. Trapped molecules either desorb within a few ms, or are taken up by the butanol phase during longer times. The water uptake and surface residence time increase with temperature above 180 K indicating melting of the butanol surface 4.5 K below the bulk melting temperature. Water uptake changes gradually across the melting point and trapped molecules are rapidly lost by diffusion into the liquid above 190 K. This indicates that liquid butanol maintains a surface phase with limited water permeability up to 5.5 K above the melting point. These surface observations are indicative of an incremental change from solid to liquid butanol over a range of 10 K straddling the bulk melting temperature, in contrast to the behavior of bulk butanol and previously studied materials.

physics.chem-ph↗

arXiv2013

First-Principles Studies of Photoinduced Charge Transfer in Noncovalently Functionalized Carbon Nanotubes

We have studied the energetics, electronic structure, optical excitation, and electron relaxation of dinitromethane molecules (CH$_{2}$N$_{2}$O$_{4}$) adsorbed on semiconducting carbon nanotubes (CNTs) of chiral index (n,0) (n=7, 10, 13, 16, 19). Using first-principles density functional theory (DFT) with generalized gradient approximations and van der Waals corrections, we have calculated adsorption energies of dinitropentylpyrene, in which the dinitromethane is linked to the pyrene via an aliphatic chain, on a CNT. A 75.26 kJ/mol binding energy has been found, which explains why such aliphatic chain-pyrene units can be and have been used in experiments to bind functional molecules to CNTs. The calculated electronic structures show that the dinitromethane introduces a localized state inside the band gap of CNT systems of n=10, 13, 16 and 19; such a state can trap an electron when the CNT is photoexcited. We have therefore investigated the dynamics of intra-band relaxations using the reduced density matrix formalism in conjunction with DFT. For pristine CNTs, we have found that the calculated charge relaxation constants agree well with the experimental time scales. Upon adsorption, these constants are modified, but there is not a clear trend for the direction and magnitude of the change. Nevertheless, our calculations predict that electron relaxation in the conduction band is faster than hole relaxation in the valence band for CNTs with and without molecular adsorbates.

physics.chem-ph↗

arXiv2013

Density Functional Theory for Protein Transfer Free Energy

We cast the problem of protein transfer free energy within the formalism of density functional theory (DFT), treating the protein as a source of external potential that acts upon the solvent. Solvent excluded volume, solvent-accessible surface area, and temperature-dependence of the transfer free energy all emerge naturally within this formalism, and may be compared with simplified "back of the envelope" models, which are also developed here. Depletion contributions to osmolyte induced stability range from 5-$10\kB T$ for typical protein lengths. The general DFT transfer theory developed here may be simplified to reproduce a Langmuir isotherm condensation mechanism on the protein surface in the limits of short-ranged interactions, and dilute solute. Extending the equation of state to higher solute densities results in non-monotonic behavior of the free energy driving protein or polymer collapse. Effective interaction potentials between protein backbone or sidechains and TMAO are obtained, assuming a simple backbone/sidechain 2-bead model for the protein with an effective 6-12 potential with the osmolyte. The transfer free energy $δg$ shows significant entropy: $d(δg)/dT \approx 20 \kB$ for a 100 residue protein. The application of DFT to effective solvent forces for use in implicit-solvent molecular dynamics is also developed. The simplest DFT expressions for implicit-solvent forces contain both depletion interactions and an "impeded-solvation" repulsive force at larger distances.

q-bio.BM↗

arXiv2013

Nanoscale Dielectric Capacitors Composed of Graphene and Boron Nitride Layers: A First Principles Study of High-Capacitance at Nanoscale

We investigate a nanoscale dielectric capacitor model consisting of two-dimensional, hexagonal h-BN layers placed between two commensurate and metallic graphene layers using self-consistent field density functional theory. The separation of equal amounts of electric charge of different sign in different graphene layers is achieved by applying electric field perpendicular to the layers. The stored charge, energy, and the electric potential difference generated between the metallic layers are calculated from the first-principles for the relaxed structures. Predicted high-capacitance values exhibit the characteristics of supercapacitors. The capacitive behavior of the present nanoscale model is compared with that of the classical Helmholtz model, which reveals crucial quantum size effects at small separations, which in turn recede as the separation between metallic planes increases.

cond-mat.mes-hall↗

arXiv2013

Ab-Initio Calculation of Molecular Aggregation Effects: a Coumarin-343 Case Study

We present time-dependent density functional theory (TDDFT) calculations for single and dimerized Coumarin-343 molecules in order to investigate the quantum mechanical effects of chromophore aggregation in extended systems designed to function as a new generation of sensors and light-harvesting devices. Using the single-chromophore results, we describe the construction of effective Hamiltonians to predict the excitonic properties of aggregate systems. We compare the electronic coupling properties predicted by such effective Hamiltonians to those obtained from TDDFT calculations of dimers, and to the coupling predicted by the transition density cube (TDC) method. We determine the accuracy of the dipole-dipole approximation and TDC with respect to the separation distance and orientation of the dimers. In particular, we investigate the effects of including Coulomb coupling terms ignored in the typical tight-binding effective Hamiltonian. We also examine effects of orbital relaxation which cannot be captured by either of these models.

physics.chem-ph↗

arXiv2013

Disentangling electronic and vibronic coherences in two-dimensional echo spectra

The prevalence of long-lasting oscillatory signals in the 2d echo-spectroscopy of light-harvesting complexes has led to a search for possible mechanisms. We investigate how two causes of oscillatory signals are intertwined: (i) electronic coherences supporting delocalized wave-like motion, and (ii) narrow bands in the vibronic spectral density. To disentangle the vibronic and electronic contributions we introduce a time-windowed Fourier transform of the signal amplitude. We find that 2d spectra can be dominated by excitations of pathways which are absent in excitonic energy transport. This leads to an underestimation of the life-time of electronic coherences by 2d spectra.

physics.bio-ph↗

arXiv2013

Missing short-range interactions in the hydrogen bond of compressed ice

Combining the Lagrangian-Laplace mechanics and the known pressure dependence of the length-stiffness relaxation dynamics, we have determined the critical, yet often-overlooked, short-range interactions in the hydrogen bond of compressed ice. This approach has enabled determination of the force constant, cohesive energy, potential energy of the vdW and the covalent segment at each quasi-equilibrium state as well as their pressure dependence. Evidencing the essentiality of the inter-electron-pair Coulomb repulsion and the segmental strength disparity in determining the asymmetric H-bond relaxation dynamics and the anomalous properties of ice, results confirmed that compression shortens and stiffens the OH bond and meanwhile lengthens and softens the covalent bond.

cond-mat.mtrl-sci↗

arXiv2014

Pariser-Parr-Pople Model based Investigation of Ground and Low-Lying Excited States of Long Acenes

Several years back Angliker et al [Chem. Phys. Lett. 1982, 87, 208] predicted nonacene to be the first linear acene with the triplet state $1^{3}B_{2u}$ as the ground state, instead of the singlet $1^{1}A_{g}$ state. However, contrary to that prediction, in a recent experimental work Tönshoff and Bettinger [ Angew. Chem. Int. Ed. 2010, 49, 4125] demonstrated that nonacene has a singlet ground state. Motivated by this experimental finding, we decided to perform a systematic theoretical investigation of the nature of the ground, and the low-lying excited states of long acenes, with an emphasis on the singlet-triplet gap, starting from naphthalene, all the way up to decacene. Methodology adopted in our work is based upon Pariser-Parr-Pople model (PPP) Hamiltonian, along with large-scale multi-reference singles-doubles configuration interaction (MRSDCI) approach. Our results predict that even though the singlet-triplet gap decreases with the increasing conjugation length, nevertheless, it remains finite till decacene, thus providing no evidence of the predicted singlet-triplet crossover. We also analyze the nature of many-particle wavefunction of the correlated singlet ground state and find that the longer acenes exhibit tendency towards a open-shell singlet ground state. Moreover, when we compare the experimental absorption spectra of octacene and nonacene with their calculated singlet and triplet absorption spectra, we observe excellent agreement for the singlet case. Hence, the optical absorption results also confirm the singlet nature of the ground state for longer acenes.

cond-mat.mtrl-sci↗

arXiv2013

Density-Dependent Onset of the Long-Range Exchange: A Key to Donor-Acceptor Properties

Quantum mechanical methods based on the density functional theory (DFT) offer a realistic possibility of first-principles design of organic donor-acceptor systems and engineered band-gap materials. This promise is contingent upon the ability of DFT to predict one-particle states accurately. Unfortunately, approximate functionals fail to align the orbital energies with ionization potentials. We describe a new paradigm for achieving this alignment. In the proposed model, an average electron-exchange hole separation controls the onset of the orbital-dependent exchange in approximate range-separated functionals. The correct description of one-particle states is thus achieved without explicit electron removal or attachment. Extensive numerical tests show that the proposed method provides physically sound orbital gaps and leads to excellent predictions of charge-transfer excitations and other properties critically depending on the tail of the electron density.

physics.chem-ph↗

arXiv2014

Electron and Hole Injection via Charge Transfer at the Topological-Insulator $Bi_{2-x}Sb_xTe_{3-y}Se_y$/Organic-Molecule Interface

As a methodology for controlling the carrier transport of topological insulators (TI's), a flexible tuning in carrier number on the surface states (SS's) of three dimensional TI's by surface modifications using organic molecules is described. The principle of the carrier tuning and its type conversion of TI's presented in this research are based on the charge transfer of holes or electrons at the TI/organic molecule interface. By employing 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4-TCNQ) as an electron acceptor or tetracyanoquinodimethane (TCNQ) as a donor for n- and p- Bi2-xSbxTe3-ySey (BSTS) single crystals, successful carrier conversion from n to p and its reverse mode is demonstrated depending on the electron affinities of the molecules. The present method provides a nondestructive and efficient method for local tuning in carrier density of TI's, and is useful for future applications.

cond-mat.mtrl-sci↗

arXiv2014

Molecule-optimized Basis Sets and Hamiltonians for Accelerated Electronic Structure Calculations of Atoms and Molecules

Molecule-optimized basis sets, based on approximate natural orbitals, are developed for accelerating the convergence of quantum calculations with strongly correlated (multi-referenced) electrons. We use a low-cost approximate solution of the anti-Hermitian contracted Schr{ö}dinger equation (ACSE) for the one- and two-electron reduced density matrices (RDMs) to generate an approximate set of natural orbitals for strongly correlated quantum systems. The natural-orbital basis set is truncated to generate a molecule-optimized basis set whose rank matches that of a standard correlation-consistent basis set optimized for the atoms. We show that basis-set truncation by approximate natural orbitals can be viewed as a one-electron unitary transformation of the Hamiltonian operator and suggest an extension of approximate natural-orbital truncations through two-electron unitary transformations of the Hamiltonian operator, such as those employed in the solution of the ACSE. The molecule-optimized basis set from the ACSE improves the accuracy of the equivalent standard atom-optimized basis set at little additional computational cost. We illustrate the method with the potential energy curves of hydrogen fluoride and diatomic nitrogen. Relative to the hydrogen fluoride potential energy curve from the ACSE in a polarized triple-zeta basis set, the ACSE curve in a molecule-optimized basis set, equivalent in size to a polarized double-zeta basis, has a nonparallelity error of 0.0154 a.u. which is significantly better than the nonparallelity error of 0.0252 a.u. from the polarized double-zeta basis set.

physics.chem-ph↗