In the present work, we investigate, for the first time, quasi 3D porous tetragonal silicon–carbon polymorphs t(SiC)₁₂ and t(SiC)₂₀ on the basis of first-principles density functional theory calculations. The structural design of these q3-t(SiC)12 and q3-t(SiC)₂₀ polymorphs follows an intuitive rational approach based on armchair nanotubes of a tetragonal SiC monolayer where C–C and Si–Si bonds are arranged in a paired configuration for retaining a 1:1 ratio of the two elements. Our calculations uncover that q3-t(SiC)₁₂ and q3-t(SiC)₂₀ polymorphs are thermally, dynamically, and mechanically stable with this lattice framework. The results demonstrate that the smaller polymorph q3-t(SiC)₁₂ shows a small band gap (∼0.59 eV), while the larger polymorph of q3-t(SiC)₂₀ displays a Dirac nodal line semimetal. Moreover, the 1D channels are favorable for accommodating Na ions with excellent (>300 mAh g^–1) reversible theoretical capacities. Thus confirming potential suitability of the two porous polymorphs with an appropriate average voltage and vanishingly small volume change (<6%) as anodes for Na-ion batteries.

Electrochemical doping of organic mixed ionic-electronic conductors is key for modulating their conductivity, charge storage and volume enabling high performing bioelectronic devices such as recording and stimulating electrodes, transistors-based sensors and actuators. However, electrochemical doping has not been explored to the same extent for modulating the mechanical properties of OMIECs on demand. Here, we report a qualitative and quantitative study on how the mechanical properties of a glycolated polythiophene, p(g3T2), change in situ during electrochemical doping and de-doping. The Young's modulus of p(g3T2) changes from 69 MPa in the dry state to less than 10 MPa in the hydrated state and then further decreases down to 0.4 MPa when electrochemically doped. With electrochemical doping-dedoping the Young's modulus of p(g3T2) changes by more than one order of magnitude reversibly, representing the largest modulation reported for an OMIEC. Furthermore, we show that the electrolyte concentration affects the magnitude of the change, demonstrating that in less concentrated electrolytes more water is driven into the film due to osmosis and therefore the film becomes softer. Finally, we find that the oligo ethylene glycol side chain functionality, specifically the length and asymmetry, affects the extent of modulation. Our findings show that glycolated polythiophenes are promising materials for mechanical actuators with a tunable modulus similar to the range of biological tissues, thus opening a pathway for new mechanostimulation devices. This work investigates the changes in the mechanical properties of glycolated polythiophenes induced by electrochemical addressing and by electrolyte concentration, due to its ability to stabilize water.

Studies of parity (P) and time-reversal (T) symmetry violations using molecules are important and attractive because they are complementary to the high-energy tests of physics beyond the Standard Model of elementary particles. The focus of our present work is to surpass the current accuracies of the quantity X, an enhancement factor for the nuclear Schiff moment (Q), and the nucleon electric dipole moments for the (TlF)-Tl-205 molecule. We obtain X = 6856 a.u. using a relativistic coupled-cluster singles and doubles and perturbative triples (CCSD(T)) approach. This new value of X improves the upper limits for Q and the proton EDM by about ten percent over the previous ones. [GRAPHICS] .

Several improvements to the previously optimized GROMACS BlueGene inner loops that evaluate nonbonded interactions in molecular dynamics simulations are presented. The new improvements yielded an 11% decrease in running time for both PME and other kinds of GROMACS simulations that use nonbonded table look-ups. Some other GROMACS simulations will show a small gain.

We address the question of constructing a protocol for replica-exchange molecular dynamics (REMD) simulations that make efficient use of the replica space, assess whether published applications are achieving such "mixing" efficiency, and provide a how-to guide to assist users to plan efficient REMD simulations. To address our first question, we introduce and discuss three metrics for assessing the number of replica-exchange attempts required to justify the use of a replica scheme and define a "transit number" as the lower bound for the length of an efficient simulation. Our literature survey of applications of REMD simulations of peptides in explicit solvent indicated that authors are not routinely reporting sufficient details of their simulation protocols to allow readers to make independent assessments of the impact of the method on their results, particularly whether mixing efficiency has been achieved. Necessary details include the expected or observed replica-exchange probability, together with the total number of exchange attempts, the exchange period, and estimates of the autocorrelation time of the potential energy. Our analysis of cases where the necessary information was reported suggests that in many of these simulations there are insufficient exchanges attempted or an insufficiently long period between them to provide confidence that the simulation length justifies the size of the replica scheme. We suggest guidelines for designing REMD simulation protocols to ensure mixing efficiency. Two key recommendations are that the exchange period should in general be larger than 1 ps and the number of exchange attempts should be chosen to significantly exceed the transit number for the replica scheme.

Based on our critique of requirements for performing an efficient molecular dynamics simulation with the particle-mesh Ewald (PME) implementation in GROMACS 4.5, we present a computational tool to enable the discovery of parameters that produce a given accuracy in the PME approximation of the full electrostatics. Calculations on two parallel computers with different processor and communication structures showed that a given accuracy can be attained over a range of parameter space, and that the attributes of the hardware and simulation system control which parameter sets are optimal. This information can be used to find the fastest available PME parameter sets that achieve a given accuracy. We hope that this tool will stimulate future work to assess the impact of the quality of the PME approximation on simulation outcomes, particularly with regard to the trade-off between cost and scientific reliability in biomolecular applications.

Producing new energetic materials is expensive. This work aims to develop a method of estimating the Chapman-Jouget detonation pressure and the detonation velocity of potential new CHNO explosives. This would allow choosing the most promising candidates for synthesis and testing thus avoiding wasting resources. This method utilizes density functional theory (DFT) and the electrostatic potential to estimate heats of formation and crystal densities. The calculations were performed on traditionally used explosives and the calculated detonation pressures and detonation velocities showed good accordance with experimental data. The calculated detonation pressures fell within ±10% and the detonation velocities within ±5% of experimental data.

Ab initio electronic structure theory is known as a useful tool for prediction of materials properties. However, majority of simulations still deal with calculations in the framework of density functional theory with local or semi-local functionals carried out at zero temperature. We present new methodological solution.s, which go beyond this approach and explicitly take finite temperature, magnetic, and many-body effects into account. Considering Ti-based alloys, we discuss !imitations of the quasiharmonic approximation for the treatment of lattice vibrations, and present an accurate and easily extendable method to calculate free ,energies of strongly anharmonic solids. We underline the necessity to going beyond the state-of-the-art techniques for the determination of effective cluster interactions in systems exhibiting mctal-to-insulator transition, and describe a unified cluster expansion approach developed for this class of materials. Finally, we outline a first-principles method, disordered local moments molecular dynamics, for calculations of thermodynamic properties of magnetic alloys, like Cr_1-x,.Al_xN, in their high-temperature paramagnetic state. Our results unambiguously demonstrate importance of finite temperature effects in theoretical calculations ofthermodynamic properties ofmaterials.

The correct determination of the ionization potential (IP) and electron affinity (EA) as well as the energy gap is essential to properly characterize a series of key phenomena related to the applications of organic semiconductors. For example, energy offsets play an essential role in charge separation in organic photovoltaics. Yet there has been a lot of confusion involving the real physical meaning behind those quantities. Experimentally the energy gap can be measured by direct techniques such as UV-Vis absorption, or indirect techniques such as cyclic voltammetry (CV). Another spectroscopic method is the Reflection Electron Energy Loss Spectroscopy (REELS). Regarding data correlation, there is little consensus on how the REELS' energy gap can be interpreted in light of the energies obtained from other methodologies such as CV, UV-Vis, or photoemission. In addition, even data acquired using those traditional techniques has been misinterpreted or applied to derive conclusions beyond the limits imposed by the physics of the measurement. A similar situation also happens when different theoretical approaches are used to assess the energy gap or employed to explain outcomes from experiments. By using a set of porphyrin derivatives as model molecules, we discuss some key aspects of those important issues. The peculiar properties of these porphyrins demonstrate that even straightforward measurements or calculations performed in a group of very similar molecules need a careful interpretation of the outcomes. Differences up to 660 meV (similar to 190 meV) are found comparing REELS (electrochemical) measurements with UV-Vis energy gaps, for instance. From the theoretical point of view, a reasonable agreement with electrochemical measurements of the IP, EA, and the gap of the porphyrins is only obtained when the calculations involve the full thermodynamics of the redox processes. The purpose of this work is to shed light on the differences and similarities of those aforementioned characterization methods and provide some insight that might help one to develop a critical analysis of the different experimental and theoretical methodologies.

Geometrical parameters, electronic structures and photophysical properties of three new triphenylamine (TPA) and diphenylamine (DPA) based electron donor materials M1-M3 (for organic solar cells) have been investigated through density functional theory (DFT) methods at the B3LYP/6-31G(d) level of the theory. TPA and DPA are used as donor moieties due to their electron donating ability while benzothiazole, cyanide and cyanomethylacetate (CMA) moieties have been taken as acceptor moieties. The time dependent-DFT (TD-DFT) method has been employed [TD-B3LYP/6-31G (d)] for the computation of excited state properties in the gas phase and in solvent (chloroform). The polarization continuum model is applied for calculations in the solvent phase. The designed molecules exhibited broad absorption in the visible and near infra-red region of spectrum with respect to a reference molecule "R" of a similar class of compounds. Based on reorganization energies calculations, these materials could act as excellent hole transport materials.

Molecular electrocatalysts for CO2-to-CO conversion often operate at large overpotentials, due to the large barrier for C-O bond cleavage. Illustrated with ruthenium polypyridyl catalysts, we herein propose a mechanistic route that involves one metal center that acts as both Lewis base and Lewis acid at different stages of the catalytic cycle, by density functional theory in corroboration with experimental FTIR. The nucleophilic character of the Ru center manifests itself in the initial attack on CO2 to form [Ru-CO2](0), while its electrophilic character allows for the formation of a 5-membered metallacyclic intermediate, [Ru-CO2CO2](0,c), by addition of a second CO2 molecule and intramolecular cyclization. The calculated activation barrier for C-O bond cleavage via the metallacycle is decreased by 34.9 kcal mol(-1) as compared to the non-cyclic adduct in the two electron reduced state of complex 1. Such metallacyclic intermediates in electrocatalytic CO2 reduction offer a new design feature that can be implemented consciously in future catalyst designs.

Molecular electrocatalysts for CO2-to-CO conversion often operate at large overpotentials, due to the large barrier for C−O bond cleavage. Illustrated with ruthenium polypyridyl catalysts, we herein propose a mechanistic route that involves one metal center that acts as both Lewis base and Lewis acid at different stages of the catalytic cycle, by density functional theory in corroboration with experimental FTIR. The nucleophilic character of the Ru center manifests itself in the initial attack on CO2 to form [Ru-CO2]0, while its electrophilic character allows for the formation of a 5-membered metallacyclic intermediate, [Ru-CO2CO2]0,c, by addition of a second CO2 molecule and intramolecular cyclization. The calculated activation barrier for C−O bond cleavage via the metallacycle is decreased by 34.9 kcal mol−1 as compared to the non-cyclic adduct in the two electron reduced state of complex 1. Such metallacyclic intermediates in electrocatalytic CO2 reduction offer a new design feature that can be implemented consciously in future catalyst designs.

The base-catalysed 1,3-proton transfer reactions in 1-methylindene have been studied theoretically in polar (water) and unpolar (cyclohexane) solvents, respectively, for two different choices of bases, namely ammonia and trimethylamine (TMA), using the SM

Atomistic simulations can complement the scarce experimental data on free energies of molecules at bio-inorganic interfaces. In molecular simulations, adsorption free energy landscapes are efficiently explored with advanced sampling methods, but classical dynamics is unable to capture charge transfer and polarization at the solid-liquid interface. Ab initio simulations do not suffer from this flaw, but only at the expense of an overwhelming computational cost. Here, we introduce a protocol for adsorption free energy calculations that improves sampling on the timescales relevant to ab initio simulations. As a case study, we calculate adsorption free energies of the charged amino acids Lysine and Aspartate on the fully hydrated anatase (101) TiO2 surface using tight-binding forces. We find that the first-principle description of the system significantly contributes to the adsorption free energies, which is overlooked by calculations with previous methods.

We report here an experimental-computational study of hydrated TiO2 anatase nanoparticles interacting with glycine, where we obtain quantitative agreement of the measured adsorption free energies. Ab initio simulations are performed within the tight binding and density functional theory in combination with enhanced free-energy sampling techniques, which exploit the thermodynamic integration of the unbiased mean forces collected on-the-fly along the molecular dynamics trajectories. The experiments adopt a new and efficient setup for electrochemical impedance spectroscopy measurements based on portable screen-printed gold electrodes, which allows fast and in situ signal assessment. The measured adsorption free energy is -30 kJ/mol (both from experiment and calculation), with preferential interaction of the charged NH3+ group which strongly adsorbs on the TiO2 bridging oxygens. This highlights the importance of the terminal amino groups in the adsorption mechanism of amino acids on hydrated metal oxides. The excellent agreement between computation and experiment for this amino acid opens the doors to the exploration of the interaction free energies for other moderately complex bionano systems.

We report here an experimental-computational study of hydrated TiO₂ anatase nanoparticles interacting with glycine, where we obtain quantitative agreement of the measured adsorption free energies. Ab initio simulations are performed within the tight binding and density functional theory in combination with enhanced free-energy sampling techniques, which exploit the thermodynamic integration of the unbiased mean forces collected on-the-fly along the molecular dynamics trajectories. The experiments adopt a new and efficient setup for electrochemical impedance spectroscopy measurements based on portable screen-printed gold electrodes, which allows fast and in situ signal assessment. The measured adsorption free energy is −30 kJ/mol (both from experiment and calculation), with preferential interaction of the charged  group which strongly adsorbs on the TiO₂ bridging oxygens. This highlights the importance of the terminal amino groups in the adsorption mechanism of amino acids on hydrated metal oxides. The excellent agreement between computation and experiment for this amino acid opens the doors to the exploration of the interaction free energies for other moderately complex bionano systems.

Alkynes have been found to be excellent ligands for Pd(0); the stability of a range of alkyne-Pd(0) complexes, and their reactivity in oxidative addition, have been investigated by DFT methods.

The mechanism of the Pd-catalyzed hydroarylation and hydrovinylation reaction of alkynes has been studied by a combination of experimental and theoretical methods (B3LYP), with an emphasis on the phosphine-free version. The regioselectivity of the hydroarylation and hydrovinylation shows unexpected differences, which could be attributed mainly to the higher steric demand of the cyclohexenyl group as compared to the phenyl group. Hydroarylation of alpha,beta-acetylenic carbonyl substrates yields a very unusual anti-Michael selectivity, which is shown to result from reaction of the nonconjugated double bond, leaving the conjugation intact. In all cases were the regioselectivities reproduced by the calculations.

Dinuclear alkynyl copper(I) complexes exhibit superior reactivity toward organic azides compared to their monomeric analogues. DFT studies indicate that the second copper center facilitates the formation of the cupracycle in the rate-determining step and stabilizes the metallacycle intermediate itself. These findings support the experimentally determined rate law and shed light on the origin of high reactivity of the in situ generated copper acetylides.

The oxidative addition of PhI to Pd-O has been studied by DFT with a continuum representation of the solvent. It is shown that the preferred number of ligands on palladium is lower than would be expected from "conventional wisdom" and the 18-electron rule. The most favored oxidative addition is obtained when Pd is coordinated by only the aryl iodide and one additional ligand in a linear arrangement. The calculations indicate that p-orbitals on the central metal are not involved in bonding in any of the complexes described herein, in good agreement with classic ligand field theory and also with a recent bonding analysis by Weinhold and Landis, but in apparent violation of the 18-electron rule.

The determination of continuum solvation models for the solvation energy of anions, was described. To investigate the reliability of the solvent model, a few explicit THF molecules were incorporated. A set of anions was chosen for which the experimental free energiesof solvation were available for both H ₂O and DMSO solutions. A major difference between the water model and the DMSO model is that the latter systematically overestimates the free energy of solvation. The full water model in Jaguar v 4.2, including also nonelectrostatic terms, gives good correlation with experimental values for energy of solvation.

Selective, direct conversion of methane to methanol might seem an impossible task since the C-H bond energy of methane is 105 kcal mol(-1) compared to the C-H bond energy for methanol of 94. We show here that the Catalytica catalyst is successful because the methanol is protected as methyl bisulfate, which is substantially less reactive than methanol toward the catalyst. This analysis suggests a limiting performance for systems that operate by this type of protection that is well above the Catalytica system.

18e R.I.P. The apparent compliance of [Pd(PPh₃)₄] ("tetrakis") with the 18-electron rule is not due to an electronic preference on the central metal. Pd is valence-saturated already by two ligands. Further ligand addition gives a minor energy gain, and is only possible due to strong back-bonding. Dispersion corrections are needed for properly describing the interactions between the ligands.

Oxidative addition of aryl chlorides to palladium has been investigated by hybrid density functional theory methods (B3LYP), including a continuum model describing the solvent implicitly. A series of para-substituted aryl chlorides were studied to see the influence of electronic effects on the reaction. It was found that the experimentally observed higher reactivity of the more electron deficient aryl chlorides is due to their ability to accept back-donation from Pd-0 and form reasonably strong pre-reactive complexes. This effect is less pronounced in the transition state; when it is measured from the pre-reactive complex, the barrier to oxidative addition is actually higher for the electron-deficient aryl chlorides, but the overall reaction barrier is still lower than for the electron-rich aryl chlorides.

Quantum mechanical (QM) results are used to establish the role of sulfuric acid solvent in facilitating the reaction between Pt(II)(bpym)Cl(2) (bpym = 2,2'-bipyrimidinyl) and methane; coordination of methane to the platinum catalyst is found to be catalyzed by the acidic medium.

Interactions between the group XII metals Zn²⁺ and Cd²⁺ and amino acid residues play an important role in biology due to the prevalence of the first and the toxicity of the second. Estimates of the interaction energies between the ions and relevant residues in proteins are however difficult to obtain. This study reports on calculated interaction energy curves for small complexes of Zn²⁺ or Cd²⁺ and amino acid mimics (acetate, methanethiolate, and imidazole) or water. Given that many applications and models (e.g., force fields, solvation models, etc.) begin with and rely on an accurate description of gas-phase interaction energies, this is where our focus lies in this study. Four density functional theory (DFT)-functionals and MP2 were used to calculate the interaction energies not only at the respective equilibrium distances but also at a relevant range of ion–ligand separation distances. The calculated values were compared with those obtained by CCSD(T). All DFT-methods are found to overestimate the magnitude of the interaction energy compared to the CCSD(T) reference values. The deviation was analyzed in terms of energy components from localized molecular orbital energy decomposition analysis scheme and is mostly attributed to overestimation of the polarization energy. MP2 shows good agreement with CCSD(T) [root mean square error (RMSE) = 1.2 kcal/mol] for the eight studied complexes at equilibrium distance. Dispersion energy differences at longer separation give rise to increased deviations between MP2 and CCSD(T) (RMSE = 6.4 kcal/mol at 3.0 Å). Overall, the results call for caution in applying DFT methods to metalloprotein model complexes even with closed-shell metal ions such as Zn²⁺ and Cd²⁺, in particular at ion–ligand separations that are longer than the equilibrium distances.

Interactions between the group XII metals Zn²⁺ and Cd²⁺ and amino acid residues play an important role in biology due to the prevalence of the first and the toxicity of the second. Estimates of the interaction energies between the ions and relevant residues in proteins are however difficult to obtain. This study reports on calculated interaction energy curves for small complexes of Zn²⁺ or Cd²⁺ and amino acid mimics (acetate, methanethiolate, and imidazole) or water. Given that many applications and models (e.g., force fields, solvation models, etc.) begin with and rely on an accurate description of gas-phase interaction energies, this is where our focus lies in this study. Four density functional theory (DFT)-functionals and MP2 were used to calculate the interaction energies not only at the respective equilibrium distances but also at a relevant range of ion–ligand separation distances. The calculated values were compared with those obtained by CCSD(T). All DFT-methods are found to overestimate the magnitude of the interaction energy compared to the CCSD(T) reference values. The deviation was analyzed in terms of energy components from localized molecular orbital energy decomposition analysis scheme and is mostly attributed to overestimation of the polarization energy. MP2 shows good agreement with CCSD(T) [root mean square error (RMSE) = 1.2 kcal/mol] for the eight studied complexes at equilibrium distance. Dispersion energy differences at longer separation give rise to increased deviations between MP2 and CCSD(T) (RMSE = 6.4 kcal/mol at 3.0 Å). Overall, the results call for caution in applying DFT methods to metalloprotein model complexes even with closed-shell metal ions such as Zn²⁺ and Cd²⁺, in particular at ion–ligand separations that are longer than the equilibrium distances.

When proteins are solvated in electrolyte solutions that contain alkali ions, the ions interact mostlywith carboxylates on the protein surface. Correctly accounting for alkali-carboxylate interactionsis thus important for realistic simulations of proteins. Acetates are the simplest carboxylates thatare amphipathic, and experimental data for alkali acetate solutions are available and can be comparedwith observables obtained from simulations. We carried out molecular dynamics simulations of alkali acetate solutions using polarizable and non-polarizable forcefields and examined the ionacetateinteractions. In particular, activity coefficients and association constants were studied in a range of concentrations (0.03, 0.1, and 1M). In addition, quantum-mechanics (QM) based energy decomposition analysis was performed in order to estimate the contribution of polarization, electrostatics, dispersion, and QM (non-classical) effects on the cation-acetate and cation-water interactions. Simulations of Li-acetate solutions in general overestimated the binding of Li⁺ and acetates. In lower concentrations, the activity coefficients of alkali-acetate solutions were too high, which is suggested to be due to the simulation protocol and not the forcefields. Energy decomposition analysis suggested that improvement of the forcefield parameters to enable accurate simulations of Li-acetate solution scan be achieved but may require the use of a polarizable forcefield. Importantly, simulations with some ion parameters could not reproduce the correct ion-oxygen distances, which calls for caution in thechoice of ion parameters when protein simulations are performed in electrolyte solutions.

In this work two different examples of water absorbtion in polymers are studied by Monte Carlo simulations. Both of them are of large technical and commercial impotance. The first example is the water absorption in polyethylene cables where the water absorption plays a crucial role in the degradation of the cable insulation and thus should be as low as possible. The second example is bio-based superabsorbents made from denatured protein where water absorption capability is the prime desired property. Methods Gibbs Ensemble Monte Carlo simulations [1] were used to study the hydration of polymers. All simulations are performed with two boxes, one of which is filled with water at the start of the simulation, whereas the other contains polymer molecules and possible ions. The polymer molecules are not allowed to swap boxes whereas the water molecules are allowed to do so thus constituting an osmotic Gibbs ensemble [2]. For the polyethylene a connectivity-altering algorithm was used whereas the protein molecules were simulated using a side-chain regrowth model in addition to traditional Monte Carlo moves. For the polyethylene, the TraPPE [3] force field was used and the protein molecules, the Amber force field [4] was used. Water was modelled using simple point charge models [5]. Electrostatic interactions are treated using Ewald summation methods. The protein molecules were of different amino acid compositions and in different conformations, e.g., β-turns and random coils obtained using the amorphous cell method[6]. Studies were made with different degrees of charging on, e.g., lysine side chains mimicking different ionization states. Results The studies of polyethylene revealed the importance of ions left from the polymerisation catalyst for the absorbtion of water and the concomitant degradation of polyethylene cable insulation. Also the absorption properties of the protein molecules is strongly related to the presence of charged groups and fully charged protein molecules absorb large amounts of water. However, neither native nor denatured protein molecules show superabsorbing properties (i.e. absorbing hundreds of times their own mass) as they show in experimental studies and the reasons for this discrepancy will be discussed. References 1. A.Z. Panagiotopoulos, Mol. Phys. 61, 813 (1987). 2. E. Johansson, K. Bolton, D.N. Theodorou, P. Ahlström, J. Chem. Phys., 126, 224902 (2007). 3. M.G. Martin, and J.I. Siepmann, J. Phys. Chem. B, 103, 4508-4517 (1999). 4. W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz Jr, D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, P.A. Kollman (1995). J. Am. Chem. Soc. 117, 5179–5197. 5. H. J. C. Berendsen, J. P. M. Postma and W. F. van Gunsteren, in Intermolecular Forces, B. Pullman, ed. (Reidel, Dordrecht, 1981) p. 331; H. J. C. Berendsen, J. R. Grigera and T. P. Straatsma, J. Phys. Chem. 91, 6269 (1987). 6. D.N. Theodorou, U.W. Suter, Macromolecules, 18, 1467 (1985).

The implementation of sputter-deposited TiOx as an electron transport layer in nonfullerene acceptor-based organic photovoltaics has been shown to significantly increase the long-term stability of devices compared to conventional solution-processed ZnO due to a decreased photocatalytic activity of the sputtered TiOx. In this work, we utilize synchrotron-based photoemission and absorption spectroscopies to investigate the interface between the electron transport layer, TiOx prepared by magnetron sputtering, and the nonfullerene acceptor, ITIC, prepared in situ by spray deposition to study the electronic state interplay and defect states at this interface. This is used to unveil the mechanisms behind the decreased photocatalytic activity of the sputter-deposited TiOx and thus also the increased stability of the organic solar cell devices. The results have been compared to similar measurements on anatase TiOx since anatase TiOx is known to have a strong photocatalytic activity. We show that the deposition of ITIC on top of the sputter-deposited TiOx results in an oxidation of Ti3+ species in the TiOx and leads to the emergence of a new O 1s peak that can be attributed to the oxygen in ITIC. In addition, increasing the thickness of ITIC on TiOx leads to a shift in the O 1s and C 1s core levels toward higher binding energies, which is consistent with electron transfer at the interface. Resonant photoemission at the Ti L-edge shows that oxygen vacancies in sputtered TiOx lie mostly in the surface region, which contrasts the anatase TiOx where an equal distribution between surface and subsurface oxygen vacancies is observed. Furthermore, it is shown that the subsurface oxygen vacancies in sputtered TiOx are strongly reduced after ITIC deposition, which can reduce the photocatalytic activity of the oxide, while the oxygen vacancies in model anatase TiOx are not affected upon ITIC deposition. This difference can explain the inferior photocatalytic activity of the sputter-deposited TiOx and thus also the increased stability of devices with sputter-deposited TiOx used as an electron transport layer.

We present a a benchmark study on density functional approximation (DFA) per-formances for predicting two-photon absorption (TPA) strengths in π-conjugatedmolecules containing electron-donating/-accepting moieties. We have incorporateda variety of meta-generalized gradient approximation (meta-GGA) functionals, in-cluding SCAN, MN15, and M06-2X, to assess their accuracy in describing the TPAproperties of the chosen set of 48 organic molecules. Quadratic response theory is em-ployed for these functionals, and their performance is compared with the previouslystudied DFAs and the coupled-cluster CC2 model (RI-CC2) is used as a reference. Adetailed analysis of the meta-GGA functionals’ performance is provided, focusing ontheir ability to capture the key electronic and structural features of the π-conjugatedsystems. Furthermore, we discuss the implications of our findings for the design ofnew materials with tailored two-photon activity and the development of more accu-rate and efficient computational methods for TPA predictions

This thesis introduces a novel computational scheme tailored for efficient calculations of nonlinear spectroscopic observables. First, a derivation and implementation of an algorithm designed to harness the linearity of the Fock matrix construction in calculating two-photon absorption cross-sections within the self-consistent field approximation is presented. Subsequently, this computational scheme is extended to the density functional theory approximation for functionals belonging to the generalized gradient approximation. Lastly the derivation and implementation of the nonlinear exchange-correlation kernel for functionals belonging to the meta generalized gradient approximation are presented for the first time.

Collectively, the advancements presented in this thesis contribute new methodologies and insights to the computational realm of nonlinear spectroscopic calculations, offering the potential for large-scale theoretical spectroscopy calculations at the level of density functional theory.

Within the density Kohn–Sham density functional theory approximation, computa-tionally tractable expressions for the isotropic second-order hyperpolarizability havebeen derived and implemented for the calculation of two-photon absorption crosssections with meta-GGA functionals for the very first time. The tensor average for-mulation presented in this work allows for the evaluation of isotropic damped cubicresponse functions using only ∼3.3 % (one-photon off-resonance regions) and ∼10%(one-photon resonance regions) of the number of kernel integrations required whenexplicitly calculating all the needed individual tensor components of the cubic re-sponse function.1 

Thermodynamically, native cellulose nano fibrils are more stable in an aggregated state. The aggregated state is however not useful from a material development perspective. Therefore much research has been done to stabilize the dispersal of the fibrils. One method to overcome this instability is by surface substitution of the O6 hydroxyl group with carboxylate groups, to make highly charged fibrils in aqueous solutions. It is therefore of much interest to understand the interaction of highly charged fibrils in aqueous solutions. In this study, we aim to model the interaction potential energy between native and surface modified cellulose nanofibrils in order to understand under what conditions the contribution from the dipole interactions can be neglected. To achieve this we propose to use a continuum electrostatic approach, modeling the electrostatic interactions as a function of the fibrils relative dipole orientation, separation, surface charge as well as ionic strength of the solution, by means of using the Poisson-Boltzmann equation.

For general exchange-correlation functionals with a dependence on the local spin densities and spin-density gradients, we provide computationally tractable expressions for the tensor-averaged quadratic response functions pertinent to the experimental observables in second-harmonic generation (SHG). We demonstrate how the tensor-averaged quantities can be implemented with reference to a derived minimal number of first- and second-order perturbed Fock matrices. Our consideration has the capability of treating a situation of resonance enhancement as it is based on damped response theory and allows for the evaluation of tensor-averaged resonant-convergent quadratic response functions using only similar to 25% (one-photon off-resonance regions) and similar to 50% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of SHG intensities in the one-photon off-resonance region are provided for a sample of makaluvamine derivatives recognized for their large nonlinear optical responses as well as a benchmark set of small- and medium-sized organic molecules.

In this Letter, we present a pioneering analysis of the density functional approximations (DFAs) beyond the generalized gradient approximation (GGA) for predicting two-photon absorption (2PA) strengths of a set of push-pull π-conjugated molecules. In more detail, we have employed a variety of meta-generalized gradient approximation (meta-GGA) functionals, including SCAN, MN15, and M06-2X, to assess their accuracy in describing the 2PA properties of a chosen set of 48 organic molecules. Analytic quadratic response theory is employed for these functionals, and their performance is compared against the previously studied DFAs and reference data obtained at the coupled-cluster CC2 level combined with the resolution-of-identity approximation (RI-CC2). A detailed analysis of the meta-GGA functional performance is provided, demonstrating that they improve upon their predecessors in capturing the key electronic features of the π-conjugated two-photon absorbers. In particular, the Minnesota functional MN15 shows very promising results as it delivers pleasingly accurate chemical rankings for two-photon transition strengths and excited-state dipole moments.

Within the self-consistent field approximation, computationally tractable expressions for the isotropic second-order hyperpolarizability have been derived and implemented for the calculation of two-photon absorption cross sections. The novel tensor average formulation presented in this work allows for the evaluation of isotropic damped cubic response functions using only similar to 3.3% (one-photon off-resonance regions) and similar to 10% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of the two-photon absorption cross section in the one-photon off-resonance and resonance regions are provided for alanine-tryptophan and 2,5-dibromo-1,4-bis(2-(4-diphenylaminophenyl)vinyl)-benzene. Furthermore, a benchmark set of 22 additional small- and medium-sized organic molecules is considered. In all these calculations, a quantitative assessment is made of the reduced and approximate forms of the cubic response function in the one-photon off-resonance regions and results demonstrate a relative error of less than similar to 5% when using the reduced expression as compared to the full form of the isotropic cubic response function.

Zinc oxide is a well-known metal oxide semiconductor with a wide direct band gap that offers a promising alternative to titanium oxide in photocatalytic applications. ZnO is studied here as quantum dots (QDs) in colloidal suspensions, where ultrasmall nanoparticles of ZnO show optical quantum confinement with a band gap opening for particles below 9 nm in diameter from the shift of the band edge energies. The optical properties of growing ZnO QDs are determined with Tauc analysis, and a system of QDs for the treatment and degradation of distributed threats is analyzed using an organic probe molecule, methylene blue, whose UV/vis spectrum is analyzed in some detail. The effect of optical properties of the QDs and the kinetics of dye degradation are quantified for low-dimensional ZnO materials in the range of 3-8 nm and show a substantial increase in photocatalytic activity compared to larger ZnO particles. This is attributed to a combined effect from the increased surface area as well as a quantum confinement effect that goes beyond the increased surface area. The results show a significantly higher photocatalytic activity for the QDs between 3 and 6 nm with a complete decolorization of the organic probe molecule, while QDs from 6 nm and upward in diameter show signs of competing reduction reactions. Our study shows that ultrasmall ZnO particles have a reactivity beyond that which is expected because of their increased surface area and also demonstrates size-dependent reaction pathways, which introduces the possibility for size-selective catalysis.

Chelated gadolinium ions, e.g., Gd-DTPA, are today used clinically as contrast agents for magnetic resonance imaging (MRI). An attractive alternative contrast agent is composed of gadolinium oxide nanoparticles as they have shown to provide enhanced contrast and, in principle, more straightforward molecular capping possibilities. In this study, we report a new, simple, and polyol-free way of synthesizing 4-5-nm-sized Gd 2O 3 nanoparticles at room temperature, with high stability and water solubility. The nanoparticles induce high-proton relaxivity compared to Gd-DTPA showing r 1 and r 2 values almost as high as those for free Gd 3+ ions in water. The Gd 2O 3 nanoparticles are capped with acetate and carbonate groups, as shown with infrared spectroscopy, near-edge X-ray absorption spectroscopy, X-ray photoelectron spectroscopy and combined thermogravimetric and mass spectroscopy analysis. Interpretation of infrared spectroscopy data is corroborated by extensive quantum chemical calculations. This nanomaterial is easily prepared and has promising properties to function as a core in a future contrast agent for MRI. 

Theoretical studies on biological systems like nucleic acid and protein have been widely developed in the past 50 years and will continue to be a topic of interest in forefronts of natural science. In addition to experimental science, computational modeling can give useful information and help us to understand biochemical issues at molecular, atomic and even electronic levels.

Deoxyribonucleic acid (DNA), the hereditary basis of life’s genetic identity, has always been major topic of discussions since its structure was built in 1953. However, harmful UV radiation from sunlight can make damage to DNA molecules and eventually give rise to DNA damaging biological consequences, like mutagenesis, carcinogenesis, and cell death. Photostability, photodamage, and photorepair are of vital importance in the photophysics and photochemistry of DNA. In this thesis, we have applied high level computer-aided theoretical methods to explore the underlying mechanisms for these three critical issues of DNA. Special attentions are paid to the following aspects: the properties of the excited states, the design of relevant computational models and the effects of biological environments.

We have systematically studied the excited state properties of DNA from single base to base pair and oligonucleotides, where the concerted base pairing and base stacking effects was found to play important roles in DNA photostability. The UV-light induced isomerization mechanism between two photoproducts of DNA photodamage has been revealed in different biological environments. In association with DNA photodamage, the related photorepair processes have been proposed for different lesions in photolyase which is a catalytic enzyme for DNA, and the calculated results well explained the experimental observations. In particular, the internal and external properties of flavin cofactors have been extensively studied by combining the electronic structure and spectroscopic calculations. We have examined the effects of the intramolecular hydrogen bond on spectroscopic properties of flavins. The good agreements with the experimental spectra indicated that the biological self-regulation acted critical role in these biological systems.

Two-photon absorption spectra of green fluorescent proteins (GFPs) often show a blue-shift band compared to their conventional one-photon absorption spectra, which is an intriguing feature that has not been well understood. We present here a systematic study on one- and two-photon spectra of GFP chromophore by means of the density functional response theory and complete active space self-consistent field (CASSCF) methods. It shows that the popular density functional fails to provide correct vibrational progression for the spectra. The non-Condon vibronic coupling, through the localised intrinsic vibrational modes of the chromophore, is responsible for the blue-shift in the TPA spectra. The cis to trans isomerisation can be identified in high-resolution TPA spectra. Our calculations demonstrate that the high level ab initio multiconfigurational CASSCF method, rather than the conventional density functional theory is required for investigating the essential excited-state properties of the GFP chromophore.

The design of a proper molecular model with a good balance between the size of the model system and the computational capacity is essential for theoretical modeling of biological systems. We have shown in this letter that the often used model system, a lumiflavin (7,8-dimethy-10-methyl-isoalloxazine), can not correctly describe geometrical and electronic structures of FADH⁻ in DNA photolyase. The intramolecular hydrogen bond between the isoalloxazine ring and the ribityl moiety is found to play a significant role in controlling photochemical properties of FADH⁻ in DNA photolyase

2-aminopyridine dimer has frequently been used as a model system for studying photochemistry of DNA base pairs. We examine here the relevance of 2-aminopyridine dimer for a Watson-Crick adenine-thymine base pair by studying UV-light induced photodynamics along two main hydrogen bridges after the excitation to the localized (1)pi pi(*) excited-state. The respective two-dimensional potential-energy surfaces have been determined by time-dependent density functional theory with Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP). Different mechanistic aspects of the deactivation pathway have been analyzed and compared in detail for both systems, while the related reaction rates have also be obtained from Monte Carlo kinetic simulations. The limitations of the 2-aminopyridine dimer as a model system for the adenine-thymine base pair are discussed. (C) 2010 American Institute of Physics. [doi:10.1063/1.3464485]

Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.

By means of ab initio calculations, we have estimated stability of 2D Me2X (Me = Mg, Ca, Sr, Ba and X = Si, Ge, Sn) in the T and Td phases, which are similar to the ones of 2D transition metal chalcogenides, in addition to their phonon spectra. The T phase is found to be more stable for 2D Ca2X, Sr2X and Ba2X, whereas the Td phase is predicted to be the ground state for 2D Mg2X. We have also discussed that imaginary frequencies in the calculated phonon spectra of 2D Me2X, which appeared in the vicinity of the Gamma point, were not necessarily associated with the dynamic instability.

This pioneering research on how specific molecules deep inside our brains form a dynamic information holarchy in phase space, linking mind and consciousness, is not only provocative but also revolutionary. Holonomic is a dynamic encapsulation of the holonic view that originates from the word “holon” and designates a holarchical rather than a hierarchical, dynamic brain organization to encompass multiscale effects. The unitary nature of consciousness being interconnected stems from a multiscalar organization of the brain. We aim to give a holonomic modification of the thermodynamic approach to the problem of consciousness using spatiotemporal intermittency. Starting with quasiparticles as the minimalist material composition of the dynamical brain where interferences patterns between incoherent waves of quasiparticles and their quantum-thermal fluctuations constrain the kinetic internal energy of endogenous molecules through informational channels of the negentropically-derived quantum potential. This indicates that brains are not multifractal involving avalanches but are multiscalar, suggesting that unlike the hologram, where the functional interactions occur in the spectral domain, the spatiotemporal binding is multiscalar because of self-referential amplification occurring via long-range correlative information. The associated negentropic entanglement permeates the unification of the functional information architecture across multiple scales. As such, the holonomic brain theory is suitable for active consciousness, proving that consciousness is not fundamental. The holonomic model of the brain’s internal space is nonmetric and nonfractal. It contains a multiscalar informational structure decoded by intermittency spikes in the fluctuations of the negentropically-derived quantum potential. It is therefore, a more realistic approach than the platonic models in phase space.

The electronic structure of a vapor-sublimated thin film of metal-free phthalocyanine (H2Pc) is studied experimentally and theoretically. An atom-specific picture of the occupied and unoccupied electronic states is obtained using x-ray-absorption spectroscopy (XAS), core- and valence-level x-ray photoelectron spectroscopy (XPS), and density-functional theory (DFT) calculations. The DFT calculations allow for an identification of the contributions from individual nitrogen atoms to the experimental N1s XAS and valence XPS spectra. This comprehensive study of metal-free phthalocyanine is relevant for the application of such molecules in molecular electronics and provides a solid foundation for identifying modifications in the electronic structure induced by various substituent groups.