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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.

The Curvature Constrained Splines (CCS) methodology has been used for fitting repulsive potentials to be used in SCC-DFTB calculations. The benefit of using CCS is that the actual fitting of the repulsive potential is performed through quadratic programming on a convex objective function. This guarantees a unique (for strictly convex) and optimum two-body repulsive potential in a single shot, thereby making the parametrization process robust, and with minimal human effort. Furthermore, the constraints in CCS give the user control to tune the shape of the repulsive potential based on prior knowledge about the system in question. Herein, we developed the method further with new constraints and the capability to handle sparse data. We used the method to generate accurate repulsive potentials for bulk Si polymorphs and demonstrate that for a given Slater-Koster table, which reproduces the experimental band structure for bulk Si in its ground state, we are unable to find one single two-body repulsive potential that can accurately describe the various bulk polymorphs of silicon in our training set. We further demonstrate that to increase transferability, the repulsive potential needs to be adjusted to account for changes in the chemical environment, here expressed in the form of a coordination number. By training a near-sighted Atomistic Neural Network potential, which includes many-body effects but still essentially within the first-neighbor shell, we can obtain full transferability for SCC-DFTB in terms of describing the energetics of different Si polymorphs.

Reversible interaction with carbon monoxide results in the onset of dynamic atropisomerism at 298 K in an otherwise static NHC-based rhodium pincer complex, [Rh(C boolean AND N boolean AND C-(CH2)(12))(CO)][BArF4] (1, ArF = 3,5-C6H3(CF3)(2)). The mechanism of this process has been comprehensively interrogated by a combination of variable-temperature NMR spectroscopy, IR spectroscopy, and computational modeling. In addition, a structural analogue of a high-energy symmetrical intermediate species-invoked in the process but not directly observed spectroscopically-has been prepared and characterized in solution and the solid-state.

Three dimensional (3D) acceptor‐donor‐acceptor (A−D‐A) type small molecules (M1, M2, M3 and M4) are theoretically investigated for optoelectronic properties. The designed molecules contain spirobifluorene as core unit linked with end capped acceptors through four four thieno‐[3,2‐b]Thiophene (TT) units. The end capped acceptors are (3‐methyl‐2‐thioxothiazolidin‐4‐one) (M1), 2‐(2‐ethylidene‐5,6‐difluoro‐3‐oxo‐2,3‐dihydroinden‐1‐ylidene)malononitrile (M2), 2‐(3‐ethyl‐4‐oxothiazolidin‐2‐ylidine)malononitrile (M3) and 2‐(2‐ethylidene‐5,6‐dicyano‐3‐oxo‐2,3‐dihydroinden‐1‐ylidene)malononitrile (M4). The photovoltaic parameters of the designed molecules are compared with the recently reported reference compound R. Among all designed molecules, M4 is a low energy gap material (2.28 eV), broad absorption which is attributed to excellent communication between strong electron withdrawing end capped acceptors through extended conjugation. All newly designed molecules have lower binding energy as compared to reference molecule R which results in higher exciton dissociation in excited state. The reorganization energy calculations indicate good charge transfer ability of the designed molecules. M4 shows the lowest λ_e (0.0022) value with respect to the reference molecule R (0.034) which signifies its enhanced electronic transport behavior. The calculated open circuit voltages (V_oc) ranges from 1.97 to 2.36 eV, 2.11 to 2.49 eV and 1.9 eV to 2.28 eV with respect to three different well known donor materials PTB7‐Th, PBDB−T and P3HT, respectively.

Due to limitations of fullerene based acceptor molecules for solar cell applications, research is recently diverted to explore non-fullerene acceptor molecules. In this regard, four new A-D-A type fused ring electron acceptor molecules (M1, M2, M3 and M4) are evaluated for their opto-electronic properties for transparent organic solar cells. These molecules contain strong electron donor undecacyclic linked with four different acceptor moieties, 2-(3-ethly-5-methylene-4-oxothiazolidin-2-yluidene)malononitrile (M1), 2-(5,6-dicyano-2-methylene-3-oxo -2,3-dihydroindene-1-ylidene)malononitrile (M2), 2-(5-methylene-6-oxo-tetrahydro-1H-cyclopenta-thiophene-4(5H)-ylidene)malononitrile (M3), and 3-ethyl-5-methylene-2-thioxothiazolidin-4-one (M4). The electronic and optical properties of these molecules are compared with the reference molecule R, which is recently reported as excellent non-fullerene based acceptor molecule. Among all molecules, M2 exhibits the maximum red shift where absorption appears 893.5 nm with B3LYP/6-31 + + G(d,p) level of theory due to highly extended conjugation between electron withdrawing end-capped acceptor moieties. The calculated Open circuit voltage (V-oc) of reference molecule R is 1.78 eV with donor polymer PTB7-Th while molecule M2 exhibits the V-oc value of 1.86 eV.

In this report we present XPS data for five amino acids (AAs) (tryptophan, methionine, glutamine, glutamic acid, and arginine) with different side chain groups measured in solid state (powder form). The theoretically and experimentally obtained chemical structure of AAs are compared. Here, we analyse and discuss C 1 s, N 1 s, O 1s and S 2p core level binding energies, FWHMs, atomic concentrations of the functional groups in AAs. The experimentally obtained and theoretically calculated ratio of atomic concentrations are compared. The zwitterionic nature of methionine and glutamine in solid state was determined from protonated amino groups in N 1s peak and deprotonated carboxylic groups in the C 1s spectrum. The obtained XPS results for AAs well correspond with previously reported data.

We studied the charging of inert surfaces (polytetrafluoroethylene, i.e., PTFE; graphite; graphene; and hydrophobic silica) using classical colloid chemistry approaches. Potentiometric titrations showed that these surfaces acquired less charge from proton-related reactions than oxide minerals. The data from batch-type titrations for PTFE powder did not show an effect of ionic strength, which was also in contrast with results for classical colloids. In agreement with classical colloids, the electrokinetic results for inert surfaces showed the typical salt level dependence. In some cases, the point of zero net proton charge as determined from mass and tentatively from acid–base titration differed from isoelectric points, which has also been previously observed, for example by Chibowski and co-workers for ice electrolyte interfaces. Finally, we found no evidence for surface contaminations of our PTFE particles before and after immersion in aqueous solutions. Only in the presence of NaCl-containing solutions did cryo-XPS detect oxygen from water. We believe that our low isoelectric points for PTFE were not due to impurities. Moreover, the measured buffering at pH 3 could not be explained by sub-micromolar concentrations of contaminants. The most comprehensive explanation for the various sets of data is that hydroxide ion accumulation occurred at the interfaces between inert surfaces and aqueous solutions.

Nitrogen doping in carbon nanostructures has attracted interest for more than a decade, and recent implementation of such structures in energy conversion systems has boosted the interest even more. Despite numerous studies, the structural conformation and stability of nitrogen functionalities in small diameter single-walled carbon nanotubes (SWNTs), and the impact of these functionalities on the electronic and mechanical properties of the SWNTs, are incomplete. Here we report a detailed study on nitrogen doping in SWNTs with diameters in the range of 0.8?1.0 nm, with well-defined chirality. We show that the introduction of nitrogen in the carbon framework significantly alters the stability of certain tubes, opening for the possibility to selectively grow nitrogen-doped SWNTs with certain chirality and diameter. At low nitrogen concentration, pyridinic functionalities are readily incorporated and the tubular structure is well pertained. At higher concentrations, pyrrolic functionalities are formed, which leads to significant structural deformation of the nanotubes and hence a stop in growth of crystalline SWNTs. Raman spectroscopy is an important tool to understand guest atom doping and electronic charge transfer in SWNTs. By correlating the influence of defined nitrogen functionalities on the electronic properties of SWNTs with different chirality, we make precise interpretation of experimental Raman data. We show that the previous interpretation of the double-resonance G?-peak in many aspects is wrong and instead can be well-correlated to the type of nitrogen doping of SWNTs originating from the p- or n-doping nature of the nitrogen incorporation. Our results are supported by experimental and theoretical data.

Hydroxyl groups are the cornerstone species driving catalytic reactions on mineral nanoparticles of Earth's crust, water, and atmosphere. Here we directly identify populations of these groups on ferrihydrite, a key yet misunderstood iron oxyhydroxide nanomineral in natural sciences. This is achieved by resolving an enigmatic set of vibrational spectroscopic signatures of reactive hydroxo groups and chemisorbed water molecules embedded in specific chemical environments. We assist these findings by exploring a vast array of configurations of computer-generated nanoparticles. We find that these groups are mainly disposed along rows at edges of sheets of iron octahedra. Molecular dynamics of nanoparticles as large as 10 nm show that the most reactive surface hydroxo groups are predominantly free, yet are hydrogen bond acceptors in an intricate network formed with less reactive groups. The resolved vibrational spectroscopic signatures open new possibilities for tracking catalytic reactions on ferrihydrite, directly from the unique viewpoint of its reactive hydroxyl groups. Ferrihydrite nanoparticles have many hydroxyl sites which can react with environmental contaminants and nutrients, but the surface structure of this common mineral is still not fully understood. Here, a combination of vibrational spectroscopy and molecular simulations identify hydroxyl groups exposed along rows at the edges of sheets of iron octahedra.

Ferrous chloride complexes [FeIILxCl] commonly attain a high-spin state independently of the supporting ligand(s) and temperature. Herein, we present the first report of a complete spin crossover with T1/2 = 80 K in [FeII(Py5OH)Cl]+ (Py5OH = pyridine-2,6-diylbis[di(pyridin-2-yl)methanol]). Both spin forms of the complex are analyzed by X-ray spectroscopy and DFT calculations.

As is well known, for plasmas of high density and modest temperature, the classical kinetic theory needs to be extended. Such extensions can be based on the Schrödinger Hamiltonian, applying a Wigner transform of the density matrix, in which case the Vlasov equation is replaced by the celebrated Wigner–Moyal equation. Extending the treatment to more complicated models, we investigate aspects such as spin dynamics (based on the Pauli Hamiltonian), exchange effects (using the Hartree–Fock approximation), Landau quantization, and quantum relativistic theory. In the relativistic theory, we first study cases where the field strength is well-beyond Schwinger critical field. Both weakly relativistic theory (gamma factors close to unity) and strongly relativistic theory are investigated, using assumptions that allow for a separation of electron and positron states. Finally, we study the so-called Dirac–Heisenberg–Wigner (DHW) formalism, which is a fully quantum relativistic theory, allowing for field strengths of the order of the Schwinger critical field or even larger. As a result, the quantum kinetic theory is extended to cover phenomena such as Zitterbewegung and electron–positron pair creation. While the focus of this review is on the quantum kinetic models, we illustrate the theories with various applications throughout the manuscript.

In recent years, a number of quantum mechanical-molecular mechanical (QM/MM) enzyme studies have investigated the dependence of reaction energetics on the size of the QM region using energy and free energy calculations. In this study, we revisit the question of QM region size dependence in QM/MM simulations within the context of energy and free energy calculations using a proton transfer in a DNA base pair as a test case. In the simulations, the QM region was treated with a dispersion-corrected AM1/d-PhoT Hamiltonian, which was developed to accurately describe phosphoryl and proton transfer reactions, in conjunction with an electrostatic embedding scheme using the particle-mesh Ewald summation method. With this rigorous QM/MM potential, we performed rather extensive QM/MM sampling, and found that the free energy reaction profiles converge rapidly with respect to the QM region size within ca. +/- 1 kcal/mol. This finding suggests that the strategy of QM/MM simulations with reasonably sized and selected QM regions, which has been employed for over four decades, is a valid approach for modeling complex biomolecular systems. We point to possible causes for the sensitivity of the energy and free energy calculations to the size of the QM region, and potential implications.

The design of artificially engineered chiral structures has received much attention, but the implementation of dynamic functions to modulate the chiroptical response of the systems is less explored. Here, we present a light-responsive G-quadruplex (G4)-based assembly in which chirality enrichment is induced, tuned, and fueled by molecular switches. In particular, the mirror-image dependence on photoactivated azo molecules, undergoing trans-to-cis isomerization, shows chiral recognition effects on the inherent flexibility and conformational diversity of DNA G4s having distinct handedness (right- and left-handed). Through a detailed experimental and computational analysis, we bring compelling evidence on the binding mode of the photochromes on G4s, and we rationalize the origin of the chirality effect that is associated with the complexation event.

Escherichia coli adenylate kinase (AdK) is a small, monomeric enzyme that synchronizes the catalytic step with the enzyme’s conformational dynamics to optimize a phosphoryl transfer reaction and the subsequent release of the product. Guided by experimental measurements of low catalytic activity in seven single-point mutation AdK variants (K13Q, R36A, R88A, R123A, R156K, R167A, and D158A), we utilized classical mechanical simulations to probe mutant dynamics linked to product release, and quantum mechanical and molecular mechanical calculations to compute a free energy barrier for the catalytic event. The goal was to establish a mechanistic connection between the two activities. Our calculations of the free energy barriers in AdK variants were in line with those from experiments, and conformational dynamics consistently demonstrated an enhanced tendency toward enzyme opening. This indicates that the catalytic residues in the wild-type AdK serve a dual role in this enzyme’s function─one to lower the energy barrier for the phosphoryl transfer reaction and another to delay enzyme opening, maintaining it in a catalytically active, closed conformation for long enough to enable the subsequent chemical step. Our study also discovers that while each catalytic residue individually contributes to facilitating the catalysis, R36, R123, R156, R167, and D158 are organized in a tightly coordinated interaction network and collectively modulate AdK’s conformational transitions. Unlike the existing notion of product release being rate-limiting, our results suggest a mechanistic interconnection between the chemical step and the enzyme’s conformational dynamics acting as the bottleneck of the catalytic process. Our results also suggest that the enzyme’s active site has evolved to optimize the chemical reaction step while slowing down the overall opening dynamics of the enzyme.

With the growing challenges of bacteria becoming resistant to conventional antibiotics, antimicrobial peptides (AMPs) may offer a potential alternative. One of the most studied AMPs, the human cathelicidin derived AMP LL-37 is notable for its antimicrobial activity even though its mechanism of action is not fully understood yet. This work investigates the interaction of LL-37 with 1-Palmitoyl-2-oleoyl-sn-glycero-3-phospho-rac-(1-glycerol) (POPG) vesicles, which were employed as a bacterial membrane model given the common presence of this phospholipid in the bacterial membrane. Experimental techniques including small angle X-ray scattering, transmission electron microscopy and dynamic light scattering were used to characterize the interactions among LL-37 and POPG. Molecular dynamics simulations complement the experimental studies with molecular-level insights into the process. LL-37 was discovered to actively and critically interact with the POPG vesicles, modifying the membrane curvature that eventually leads to structural transformations from vesicles to mixed micelles. The results shed light on the mechanisms underlying the interactions among LL-37 and bacteria mimetic vesicles and can guide the further development of AMP based antimicrobial materials and therapies.

We present an extension of a Redfield approach for calculating spin-spin relaxation rates of zero-field nuclear quadrupole resonance (NQR) coherences, which was published in [Kruk et al., PCCP, 2018, 20, 23414-23426]. The oversimplification of the secular approximation made in the recent paper makes the calculation invalid for zero-field NQR and has led to partially large deviations between predicted and experimental data from ²⁰⁹Bi-containing molecular crystals. Furthermore, these deviations led to speculations about an additional dipole-dipole relaxation mechanism besides the main electric field gradient (EFG) fluctuations. Here, we demonstrate how a complete application of the Redfield relaxation expression eliminates the deviation from experimental data without the need for additional assumptions. In particular, we point out the important role of off-diagonal elements in the Redfield relaxation matrix within the 3/2-1/2 block appearing due to degenerate energy levels. The resulting coupling between single and double coherence spin density elements leads to a faster coherence decay than for all other transitions. The pseudo rotational model for EFG fluctuations, as proposed in the earlier publication and usually applied for isotropic liquids, is extended in a second analysis by introducing a vibrational mode to account for the case of crystalline solids.

This work presents Atomistic Topology Operations in MATLAB (atom), an open source library of modular MATLAB routines which comprise a general and flexible framework for manipulation of atomistic systems. The purpose of the atom library is simply to facilitate common operations performed for construction, manipulation, or structural analysis. Due to the data structure used, atoms and molecules can be operated upon based on different chemical names or attributes, such as atom- or molecule-ID, name, residue name, charge, positions, etc. Furthermore, the Bond Valence Method and a neighbor-distance analysis can be performed to assign many chemical properties of inorganic molecules. Apart from reading and writing common coordinate files (.pdb, .xyz, .gro, .cif) and trajectories (.dcd, .trr, .xtc; binary formats are parsed via third-party packages), the atom library can also be used to generate topology files with bonding and angle information taking the periodic boundary conditions into account, and supports basic Gromacs, NAMD, LAMMPS, and RASPA2 topology file formats. Focusing on clay-mineral systems, the library supports CLAYFF (Cygan, 2004) but can also generate topology files for the INTERFACE forcefield (Heinz, 2005, 2013) for Gromacs and NAMD.

This thesis focus on the analysis of spin-lattice NMRD relaxation profilesmeasured in various complex systems such as proteins, zeolites and ionicliquids. Proton, deuterium and fluoride T1-NMRD relaxation profiles wereobtained from a fast-field cycling (FFC) instrument. It is found that alsopossible to obtain NMRD profiles from the molecular dynamics (MD)simulation trajectories. NMRD Profiles were analyzed by using differentrelaxation models, such as the Solomon-Bloembergen-Morgan (SBM) theoryand the Stochastic Liouville (SL) theory.

Paper I described the hydration of protein PrxV obtained from a MDsimulation, and compared with the picture emerges from an analysis byusing a generally accepted relaxation model [appendix C]. The result showsthat the information from NMRD analysis is an averaged picture of watermolecules with similar relaxation times; and the MD simulations containsinformation of all types of interested water molecules with differentresidence times.

In paper II NMRD profiles have been used to characterize the hydration ofthe oxygen-evolving complex in state S1 of photosystem II. NMRDexperiments were performed on both intact protein samples and Mndepletedsamples, and characteristic dispersion difference were foundbetween 0.03 MHz to 1 MHz; approximately. Both the SBM theory and theSL theory have been used to explain this dispersion difference, and it isfound that this is due to a paramagnetic enhancement of 1-2 water moleculesnearby ~10 Å from the spin center of the Mn4CaO5 cluster. The result showsthe reorientation of the molecular cluster is in μs time interval. Whencompare these two theories, the SL theory presented a better interpretationbecause parameters obtained from the SBM theory shows they didn’t fulfilthe presupposed perturbation criterion (the Kubo term).

Paper III deals with the water dynamics in the restricted/confined spaces inthe zeolite samples (H-ZSM-5 and NH4-ZSM-5) and obtained by proton anddeuterium spin-lattice NMRD profiles. The results show that the spin-latticeNMRD can be used to characterize various zeolites. The temperature has aweak effect on the relaxation rate R1, but the change of different counter ionsmay change the hydration and the translational diffusion pores and givedifferent R1.

Proton and fluoride NMRD profiles and MD simulations were both used tostudy the dynamics of BMIM[PF6] in paper IV. Results indicate the reorientation of the molecules are in the ns time regime, and the effectivecorrelation time obtained from 1H and 19F are the same. From the MDsimulation it is found the reorientation of [PF6]- ions is much faster (in ps)compare with BMIM+ ion which moves in the ns time range.

With previous results, the FFC NMRD profiles are indeed very informativetools to study the molecular dynamics of complex systems. The MDsimulation can be used as a complementary method to obtain detailedinformation. By combine these two methods, it provide a more colorfulpicture in the study of protein hydration and liquid molecular dynamics.

The water dynamics in the confined space of the zeolite ZSM-5 has bee ninvestigated by means of the field dependence of ¹H- and ²H- spin-lattice relaxation rates using a 1T Stelar FFC2000 fast field-cycling instrument. The NMRD analysis of  the experimental results indicates that the characteristic time dependence ( 50 ns to 1-2.4 μs) is due to water translational diffusion in narrow pores. The temperature dependence of the spin-lattice relaxation rates is weak.Zeolites with different counter ions( H⁺, NH₄⁺ change the water hydration and the water translational diffusion in the pores drastically. The Zeolite-NH₄⁺ slow down the water motion with a factor of 2.The NMRD profiles show somewhat stretched character and is described by two Lorenzian which indicates that the distribution of pore sizes is broaden.The water ¹H and ²H spin lattice relaxation profiles give qualitatively information about water hydration in zeolites with different counter ions and is expected also to indicate structural changes of the zeolites. 

Proton/Fluoride spin-lattice nuclear magnetic relaxation dispersion(NMRD) measurements of 1-Butyl-3-methylimidazolium-hexa fluorophosphate (BMIM[PF₆])have been carried out using a 1T Stelar FFC2000 fast-field-cycling instrument at proton Larmor frequencies ranging from 10 kHz to 40 MHz and at different temperatures. The NMRD profiles are interpreted by means of a simple relaxation modelbased on the inter- and intra-molecular dipole dipole relaxation mechanims. Using an atomic and a coarse-grained (CG)Molecular Dynamics (MD) simulations at temperature 323 K the relevant dipole-dipole correlation functions are calculated. The result indicate that the NMRD profiles can be rationalized using a combination of intra and inter molecular dipole-dipole couplings. However, both are mainly modulated by molecular reorientation whereas translation diffusion plays a minor role. The molecular reorientation dynamics  of BMIM[PF₆] ,BMIM⁺ ion are in the nano secondtime regime whereas the reorientation of  [PF6]^- is much faster and loses its correlation in the ps regime. The relaxation mechanism for  [PF6]^- is H-F inter-molecular dipole-dipole coupling which is modulated by the reorientation of  the H-containing molecule.

Four Donor-Acceptor-Donor (D-A-D) type of donor molecules (M1-M4) with triphenylamine (TPA) as donor moiety, thiophene as bridge, and thiazolothiazole as acceptor unit were designed and its photovoltaic parameters were equated with reference molecule R. DFT functional CAM-B3LYP/6-31G (d,p) was found best for geometry optimization and TD-CAM-B3LYP/6-31G (d,p) was found suitable for excited state calculations. Among designed donor molecules, M4 manifests suitable lowest band gap of 4.73 eV, frontier molecular orbital energy levels as well as distinctive broad absorption of 455.3 nm due to the stronger electron withdrawing group. The electron-withdrawing substituents contribute to red shifts of absorption spectra and better stabilities for designed molecules. The theoretically determined reorganization energies of designed donor molecules suggested excellent charge mobility property. The lower (e) values in comparison with (h) illustrated that these four donor materials would be ideal for electron transfer and M4 would be best amongst the investigated molecules with lowest (e) of 0.0177. Furthermore, the calculated Voc of M4 is 2.04 V with respect to PC60BM (phenyl-C61-butyric acid methyl ester). This study revealed that the designed donor materials are suitable and recommended for high performance organic solar cell devices.

Theoretical analysis of physical properties of organic solar cells (OSCs) are important in order to reveal the correlation between power conversion efficiencies (PCE), structure and properties. Five new A-D-A type small molecules M-1, M-2, M-3, M-4, and M-5 were designed by using dithienopyrrole (DTP) as electron rich donor unit with different types of pi-spacers and end capped acceptor units. Functional MPW1PW91/6-31G(d,p) level of theory was used to optimize the geometry of all molecules. For excited state calculation TD-MPW1PW91/6-31G(d,p) level of theory was used. The geometries, electronic structures, dipole moment, open circuit voltage, reorganization energies and charge transport properties of designed molecules M-5) have been scrutinized comparing with the reported compound R. The results revealed that the HOMO energy levels of molecules M-1, M-2, M-3, and M-5 were lower while M-4 was of high energy level thus facilitate the donation of electron as compared to references molecule R. While LUMO energy level of all the molecules were slightly high energy due electron withdrawing effects of spacer and acceptor moiety. Highest energy gap of HOMO-LUMO was observed in M-1 which was 2.48 eV and M-3 showed low energy gap (2.11 eV) as compared to other designed molecules. All molecules showed low values for lambda(e), so they have high rate of electron transfer as compared to R. All designed molecules exhibited higher value of dipole moment as compared to reference molecule R except M-1. Higher value of dipole moment of donor molecules contrary to reference means good solubility towards organic solvents which is beneficial for further solar cell device fabrication. All designed molecules show higher V-oc values except M-4 which has comparable V-oc with respect to reference molecule R. In short, choice of appropriate electron withdrawing and donating groups is very important for improving power conversion efficiencies of OSCs.

Rates of oxygen-isotope exchange were measured in the tetrasiliconiobate ion [H2+xSi4Nb16O56]((14-x)-) to better understand how large oxide ions interact with water. The molecule has 19 nonequivalent oxygen sites and is sufficiently complex to evaluate hypotheses derived from our previous work on smaller clusters. We want to examine the extent to which individual oxygen atoms react independently with particular attention given to the order of protonation of the various oxygen sites as the pH decreases from 13 to 6. As in our previous work, we find that the set of oxygen sites reacts at rates that vary over approximately 104 across the molecule at 6 < pH < 13 but with similar pH dependencies. There is NMR evidence of an intra-or intermolecular reaction at pH similar to 7, where new peaks began to slowly form without losing the O-17 isotopic tag, and at pH <= 6 these new peaks formed rapidly. The oxygen atoms bonded to silicon atoms began to isotopically exchange at pH 9 and below. The 17O NMR peak positions also vary considerably with pH for some, but not all, nonequivalent oxygen sites. This variation could be only partly accounted by electronic calculations, which indicate that oxygen atoms should shift similarly upon protonation. Instead, we see that some sites change enormously with pH, whereas other, similarly coordinated oxygen atoms are less affected, suggesting that either some protons are exchanging so rapidly that the oxygen sites are seeing an averaged charge, or that counterions are modulating the effect of the coordinated protons.

N-heterocyclic compounds have extensive biological and pharmaceutical applications. 8-Hydroxyquinoline (8-HQ) also plays a significant role in many fields of life. The excellent biological significance of the 8-HQ prompted us to extend the DFT based studies. The frontier molecular orbitals (FMOs), UV-VIS and solvation model based studies remained unknown. Therefore, we intended to study the natural bond orbital, FMOs, UV-VIS, thermodynamic properties and medium influence on solvation energies, dipole moment, FTIR and FT-Raman using polarizable continuum model (PCM) and density-based solvation model (SMD). The electronic properties of molecule were calculated by M06-2X/6-31G (d,P) and B3LYP/6-31G (d,p) level of theories. The solvent influence on the geometric parameters, FT-IR and FT-Raman were studied by B3LYP /6-31G(d) method. A good correspondence is found between the optimized parameters and the reported X-ray data. Natural bond orbital reveals that the maximum stabilization energy reached up to 39.64kJ/mol which is responsible for extra stability of the molecule. In solvated 8-HQ, a significant medium effects on FT-IR and FT-Raman intensities is observed. The intensities enhanced from gas to solvent phase. The solvation free energies are found to be -28.710 and -39.456 kJ/mol in PCM and SMD models respectively. FMOs suggested that this molecule contain less hardness and larger softness values. These findings reveal that the molecule might be bioactive.

Background: Insulin receptor kinase (IRK) and Insulin-like growth factor 1 receptor kinase (IGF-1RK) are two important members in the large class of tyrosine kinase receptors. They play pivotalroles in the regulation of glucose homeostasis, cell proliferation, differentiation, motility, andtransformation. Their dysfunctions are linked to diabetes, rheumatoid arthritis and many cancers.Although their regulatory mechanisms have been widely studied experimentally, the atomisticdetails are still poorly understood, especially for the influences caused by activation loop (A-loop)phosphorylation.Methods: Molecular dynamics (MD) and alchemical free energy simulations are carried out tounderstand mechanisms underlying the kinase proteins regulation and their thermodynamic basis.To capture a full picture about the entire kinase catalytic cycle, different functional steps areconsidered, i.e., conformational transition, substrate binding, phosphoryl transfer and productrelease. The effects of the A-loop phosphorylation on protein’s dynamics, structure, stability, andfree energy landscape are examined by various analysis methods, including principle componentanalysis (PCA), motion projection, dynamical network analysis and free energy perturbation.Results: The main findings are: 1) A-loop phosphorylation shifts the kinase conformationalpopulation to the active one by changing the electrostatic environments in the kinase apo form, 2)allosterically fine-tunes the orientation of the catalytic residues mediated by the >C-helix in thereactant and product binding states, and 3) thermodynamically favors the kinase catalysis presentedby a catalytic-cycle-mimic free energy landscape. An integrated view on the roles of A-loopphosphorylation in kinase allostery is developed by incorporating kinase’s dynamics, structuralinteractions, thermodynamics and free energy landscape. In addition, new soft-core potentials(Gaussian soft-core) and protocols are developed to conduct accurate and efficient alchemical freeenergy calculations.Conclusions: The entire catalytic cycle is examined by MD and free energy calculations andcomprehensive analyses are conducted. The findings from the studied kinases are general and canbe implemented to the other members in IRK family or even to more non-homologous familiesbecause of the conservation of the characteristic residues between their A-loop and >C-helix. Inaddition, the Gaussian soft-core potentials provide a new tool to perform alchemical free energycalculations in an efficient way.

Despite the importance of kinases' catalytic activity regulation in cell signaling, detailed mechanisms underlying their activity regulation are poorly understood. Herein, using insulin-like growth factor 1 receptor kinase (IGF-1RK) as a model, the mechanisms of kinase regulation by its activation loop (A-loop) phosphorylation were investigated through molecular dynamics (MD) and alchemical free energy simulations. Analyses of the simulation results and free energy landscapes determined for the entire catalytic cycle of the kinase revealed that A-loop phosphorylation affects each step in the IGF-1RK catalytic cycle, including conformational change, substrate binding/product release and catalytic phosphoryl transfer. Specifically, the conformational equilibrium of the kinase is shifted by 13.2 kcal mol−1 to favor the active conformation after A-loop phosphorylation, which increases substrate binding affinity of the activated kinase. This free energy shift is achieved primarily viadestabilization of the inactive conformation. The free energy of the catalytic reaction is also changed by 3.3 kcal mol−1 after the phosphorylation and in the end, facilitates product release. Analyses of MD simulations showed that A-loop phosphorylation produces these energetic effects by perturbing the side chain interactions around each A-loop tyrosine. These interaction changes are propagated to the remainder of the kinase to modify the orientations and dynamics of the αC-helix and A-loop, and together yield the observed free energy changes. Since many protein kinases share similar interactions identified in this work, the mechanisms of kinase allostery and catalysis unraveled here can be applicable to them.

In alchemical free energy (FE) simulations, annihilation and creation of atoms are generally achieved with the soft-core potential that shifts the interparticle separations. While this soft-core potential eliminates the numerical instability occurring near the two end states of the transformation, it makes the hybrid Hamiltonian vary nonlinearly with respect to the parameter λ, which interpolates between the Hamiltonians representing the two end states. This complicates FE estimation by Bennett acceptance ratio (BAR), free energy perturbation (FEP), and thermodynamic integration (TI) methods, thus reducing their calculation efficiency. In this work, we develop a new type of repulsive soft-core potential, called Gaussian soft-core (GSC) potential, with two parameters controlling its maximum and width. The main advantage of this potential is the linearity of the hybrid Hamiltonian with respect to λ, thus permitting the direct application of BAR, FEP, TI, and other variant FE methods. The accuracy and efficiency of the GSC potential are demonstrated by comparing the free energies of annihilation determined for 13 small molecules and an alchemical mutation of a protein side chain. In addition, in combination with a TI integrand (∂H/∂λ) estimation strategy, we show that GSC can considerably reduce the number of λ simulations compared to the commonly used separation-shifted soft-core potential.

Molecular docking plays an important role in drug discovery as a tool for the structure-based design of small organic ligands for macromolecules. Possible applications of docking are identification of the bioactive conformation of a protein−ligand complex and the ranking of different ligands with respect to their strength of binding to a particular target. We have investigated the effect of implicit water on the postprocessing of binding poses generated by molecular docking using MM-PB/GB-SA (molecular mechanics Poisson−Boltzmann and generalized Born surface area) methodology. The investigation was divided into three parts: geometry optimization, pose selection, and estimation of the relative binding energies of docked protein−ligand complexes. Appropriate geometry optimization afforded more accurate binding poses for 20% of the complexes investigated. The time required for this step was greatly reduced by minimizing the energy of the binding site using GB solvation models rather than minimizing the entire complex using the PB model. By optimizing the geometries of docking poses using the GB^HCT+SA model then calculating their free energies of binding using the PB implicit solvent model, binding poses similar to those observed in crystal structures were obtained. Rescoring of these poses according to their calculated binding energies resulted in improved correlations with experimental binding data. These correlations could be further improved by applying the postprocessing to several of the most highly ranked poses rather than focusing exclusively on the top-scored pose. The postprocessing protocol was successfully applied to the analysis of a set of Factor Xa inhibitors and a set of glycopeptide ligands for the class II major histocompatibility complex (MHC) A^q protein. These results indicate that the protocol for the postprocessing of docked protein−ligand complexes developed in this paper may be generally useful for structure-based design in drug discovery.

Six Acceptor-Donor-Acceptor (A-D-A) types molecules with dimethyl dithieno[3, 2-b:2',3'-d]silole) -2,6-diyl (DTS) (M-1-M-3) and dimethyl cyclopenta [2, 1-b;3,4-b]-dithiophene (CPDT) (M-4-M-6) core flanged by different acceptor units through methylthiophene bridge are evaluated as donor materials for photovoltaic applications. The photovoltaic properties of M-1-M-3 and M-4-M-6 are compared with standard RaRc and R-b,R-d respectively. Geometry optimization was performed with CAM-B3LYP/6-31G (d) level of theory. TD-CAM-B3LYP has been employed for the estimation of excited state properties of the molecules. M-1, M-2, M-3 and M-4, M-5, M-6 symbolized suitable frontier molecular orbital's (FMO's) energy levels with broad absorption spectra. The electron withdrawing substituents impart red shift in absorption spectra along with good consistancy of designed donor molecules. Reorganization energies of donor molecules (M-1-M-6) showed ideal properties of charge mobility. M-1 and M-4 illustrated lowest le values as compared to lambda(h), thus dictated that designed donor molecules are of good choice for their electron donating ability. Furthermore, M-2 and M-6 demonstrated shortest Eg of 3.7 and 3.72 eV among HOMO and LUMO energy levels.

Our understanding of the rotary-coupling mechanism of F-1-ATPase has been greatly enhanced in the last decade by advances in X-ray crystallography, single-molecular imaging, and theoretical models. Recently, Volkan-Kacso and Marcus [S. Volkan-Kacso, R. A. Marcus, Proc. Natl. Acad. Sci. U.S.A. 112, 14230 (2015)] presented an insightful thermodynamic model based on the Marcus reaction theory coupled with an elastic structural deformation term to explain the observed gamma-rotation angle dependence of the adenosine triphosphate (ATP)/ adenosine diphosphate (ADP) exchange rates of F-1-ATPase. Although the model is successful in correlating single-molecule data, it is not in agreement with the available theoretical results. We describe a revision of the model, which leads to consistency with the simulation results and other experimental data on the F-1-ATPase rotor compliance. Although the free energy liberated on ATP hydrolysis by F-1-ATPase is rapidly dissipated as heat and so cannot contribute directly to the rotation, we show how, nevertheless, F-1-ATPase functions near the maximum possible efficiency. This surprising result is a consequence of the differential binding of ATP and its hydrolysis products ADP and P-i along a well-defined pathway.

Electronic-structure calculations show that the e-isomer of the polyoxoaluminate ion in the Keggin structure [AlO4-(Al(OH)(2)-(H2O))(12)](7+) is the thermodynamically favoured one. Direct interconversion between the epsilon- and delta-isomers via cap rotation has a prohibitively high energy barrier in vacuo, suggesting that isomerisation in solution either proceeds via a dissolution-precipitation pathway, or that solvation and/or coordination to counterions reduces the barrier significantly. The implications for the formation of the [Al2O8Al28(OH)(56)(H2O)26](18+) ion are discussed.

Density functional theory is used to explore the locus and consequences of protonation in [Zn₄(HO)₂(PW₉O₃₄)₂]¹⁰⁻. The results are used to explain recent observations regarding the contrasting pH effects on the water-ligand exchange in [Mn₄(H₂O)₂(P₂W₁₅O₅₆)₂]¹⁶⁻ and [Co₄(H₂O)₂(P₂W₁₅O₅₆)₂]¹⁶⁻, and the general effect of protonation on solvent exchange in metal oxides is discussed.

The chemical step of Shikimate Kinase Helicobacter pylori, involving the transfer of a phosphoryl group, has been studied by using quantum mechanical and molecular mechanical (QM/MM) methods. Understanding the mechanism of this chemical step, present in bacteria and other microorganisms but absent in humans, can lead to the development of novel drugs for the treatment of common diseases caused by those pathogenic organisms. Different mechanisms including associative, dissociative, and concerted have been proposed up to now but there is not a consensus on the type of pathway that the reaction follows. Herein, we found that the mechanism has features from the associative and concerted types. An analysis of the free energy landscape of the chemical step reveals that the reaction is a two-step process without a well-defined intermediate state.

We report solid-state 27Al NMR spectroscopic results for the sulfate salt of the γ-Al13 Keggin cluster, γ-[AlO4Al12(OH)25(OH2)11][SO4]3·[H2O]14, that provide a spectroscopic signature for partial hydrolysis of this Keggin-type cluster. In 27Al multiple-quantum magic-angle spinning NMR spectra, all 13 Al positions of the cluster are at least partially resolved and assigned with the aid of density functional theory (DFT) calculations of the 27Al electric field gradients. The isotropic chemical shift of the single tetrahedral site, 75.7 ppm, is nearly identical to that reported for solutions from which the cluster crystallizes. Reflecting broadly similar coordination environments, the octahedral Al show mostly small variations in isotropic chemical shift (+7 to +11 ppm) and quadrupolar coupling constant (CQ; 6–7.5 MHz), except for one resonance that exhibits a much smaller CQ and another site with a larger value. DFT calculations show that deprotonation of a terminal water ligand, to form an η-OH group, causes a large reduction in the 27Al CQ, allowing assignment of a distinct, narrow peak for octahedral Al to this hydroxyl-terminated site. This result suggests a relationship between octahedral 27Al NMR line width and hydrolysis for solids prepared from Keggin-type clusters.

The complex solution behavior of polymer brushes is key to control their properties, including for biomedical applications and catalysis. The swelling behavior of poly(dimethyl aminoethyl methacrylate) (PDMAEMA) and poly(2-(methacryloyloxy)ethyl trimethylammonium chloride) (PMETAC) in response to changes in pH, solvent, and salt types has been investigated using atomistic molecular dynamics simulations. PDMAEMA and PMETAC have been selected as canonical models for weak and strong polyelectrolytes whose complex conformational behavior is particularly challenging for the development and validation of atomistic models. The GROMOS-derived atomic parameters reproduce the experimental swelling coefficients obtained from ellipsometry measurements for brushes of 5–15 nm thickness. The present atomistic models capture the protonated morphology of PDMAEMA, the swollen and collapsed conformations of PDMAEMA and PMETAC in good and bad solvents, and the salt-selective response of PMETAC. The modular nature of the molecular models allows for the simple extension of atomic parameters to a variety of polymers or copolymers.

We have investigated the computation of O-17 NMR chemical shifts of a wide range of polyoxometalates using density functional theory. The effects of basis sets and exchange-correlation functionals are explored, and whereas pure DFT functionals generally predict the chemical shifts of terminal oxygen sites quite well, hybrid functionals are required for the prediction of accurate chemical shifts in conjunction with linear regression. By using PBE0/def2-tzvp//PBE0/cc-pvtz(H-Ar), lanl2dz(K-) we have computed the chemical shifts of 37 polyoxometalates, corresponding to 209 O-17 NMR signals. We also show that at this level of theory the protonation-induced pH dependence of the chemical shift of the triprotic hexaniobate Lindqvist anion, [HxNb6O19]((8-x)), can be reproduced, which suggests that hypotheses regarding loci of protonation can be confidently tested.

We report high-frequency (up to 219 GHz) and correspondingly high-field electron paramagnetic resonance spectra and X-ray crystal structure of [Co4O4(pyridine)(4)(acetate)(4)](+) ([Co4O4(py)(4)(OAc)(4)](+)) that serves as a structural and spectroscopic model of cobalt-oxide films that are capable of oxidizing water. These results are, in large part, consistent with those from our earlier, lower-frequency study and serve to benchmark future high-field studies on paramagnetic states of the catalyst film. (C) 2013 Published by Elsevier Ltd.

Electroactive membranes are attracting attention due to their piezo-, pyro-, and ferro-electric properties. Here we report the fabrication of electroactive membranes from poly(vinylidene fluoride-trifluoroethylene) P(VDF-TrFE), i.e. co-polymers of vinylidene fluoride and trifluoroethylene. A new P(VDF-TrFE)/Polyvinylpyrrolidone (PVP)/Dimethylacetamide (DMAc)/water system was used to tailor the membranes’ structure. Since hot treatment in the air could induce defect on membrane structure (i.e., fracture, shrinkage, and rolling), the annealing was conducted in the glycerin. Thanks to the high boiling point and moderate surface tension of glycerin, the integrity of P(VDF-TrFE) membranes was preserved during the annealing process. X-ray diffraction, Fourier transform infrared spectroscopy, differential scanning calorimetry, and scanning electron microscopy experiments revealed that the relative abundance of the β–crystalline phase increased with the annealing temperature when the latter was above the Curie temperature. P(VDF-TrFE) membranes annealed at 130 °C exhibited high crystallinity with grain-like surface, which resulted from multiple stacks of edge-on lamellae, and possessed excellent physicochemical properties of filtration. The anti-fouling performance of pristine and annealed P(VDF-TrFE) membranes was tested by dead-end filtration with a 13.5 mg/L humic acid (HA) solution. Annealed P(VDF-TrFE) membranes achieved greater fluxes and had superior anti-fouling properties, which was attributed to the weaker hydrophobic attraction between HA and the aligned β–phase crystals. This work provides a facile method for designing highly crystalline P(VDF-TrFE) membranes with potential applications in filtration systems, smart wearable devices, and medicine.

Snowflakes and ordinary hexagonal ice were studied measuring water proton spin–lattice relaxation rate R1(ωI)-nuclear magnetic resonance dispersion (NMRD) profiles at proton Larmor frequencies ranging from 1 to 30 MHz and at different temperatures ranging from −2◦C to −10◦C. The spin–spin relaxation rate 1/ 1/T2(ωI) was determined at a single Larmor frequency of 16.3 MHz. The high-field wing of the proton R1(ωI)-NMRD profile was characterised by two parameters: a correlation time τc which described the dipole–dipole spectral density, and the relaxation rate at low fields R ^max _real (0) which was determined from T ₂ . The correlation time τc depended on the dynamic model used. A rotation diffusion model yield approximatively 3μs at −3◦C to about 5μs at 10◦C, whereas for a more realistic six-site discrete exchange model, the correlation times decreased slightly to about 80% for the same temperature interval. Proton dipole–dipole interactions were divided into intramolecular and intermolecular contributions where the intermolecular contribution was about 0.4–0.8 × the intramolecular contribution. It was not possible to discriminate between the dynamic models or to detect ice/water interface effects by comparing the NMRD data from snowflakes with ordinary hexagonal ice data.

Reaction of [Ir(COD)(py-(IBu)-Bu-t)](+) (py-(IBu)-Bu-t = 3-tert-butyl-1-picolylimidazol-2-ylidene) with acetonitrile results in reversible intramolecular C-H bond activation of the NHC ligand and formation of [Ir(g(2):g 1-C8H13)(py-ItBu’)(NCMe)](+). Coordinated COD acts as an internal hydride acceptor and acetonitrile coordination offsets the otherwise unfavourable thermodynamics of the process.

Computational study on four Acceptor-Donor-Acceptor (A-D-A) type of donor molecules namely, dimethyl cyanoacetate terthiophene di(methylthiophene) benzo[1,2-b: 4,5-b'] dithiophene (DMCATDMTBDT) (M1), methylrhodanine terthiophene di (methylthiophene) benzo[1,2-b: 4,5-b'] dithiophene (MRTDMTBDT) (M2), dimethyl cyanoacetate terthiophene di (fluoromethyl thiophene) benzo[1,2-b: 4,5-b'] dithiophene (DMCATDFMTBDT) (M3), and methylrhodanine terthiophene di (fluoromethyl thiophene) benzo[1,2-b: 4,5-b'] dithiophene (MRTDFMTBDT) (M4) was carried out and their photovoltaic properties were associated with methyl cyanoacetate terthiophene di (methoxy) benzo[1,2-b: 4,5-b'] dithiophene (DCAO3TBDT) (R1) and methylrhodanine terthiophene di (methoxy) benzo[1,2-b: 4,5-b'] dithiophene (DR3TBDT) (R2). For the geometry optimization DFT functional CAM B3LYP/6-31G(d) was found to be the best choice, hence TD-CAM B3LYP/631G(d) was opted for the calculation of excited state of the molecules. M3 and M4 represented appropriate frontier molecular orbital energy levels and broad absorption band. The reorganization energies of the designed molecules illustrated excellent charge mobility property. The lower le values as compared to lambda(i) illustrate that the designed donor molecules are better electron donors. M4 was found as champion molecules with the lowest le (0.01601) value. The Voc value of M3 and M4 are 2.74 eV and 2.63 eV respectively with respect to the energy levels of PC60BM (acceptor).

Binders, which maintain the structural integrity of electrodes, are critical components of lithium-based rechargeable batteries (LBRBs) that significantly affect battery performances, despite accounting for 2 to 5 wt% (up to 5 wt% but usually 2 wt%) of the entire electrode. Traditional polyvinylidene fluoride (PVDF) binders that interact with electrode components via weak van der Waals forces are effective in conventional LBRB systems (graphite/LiCoO2, etc.). However, its stable fluorinated structures limit the potential for further functionalization and inhibit strong interactions towards external substances. Consequently, they are unsuitable for next-generation battery systems with high energy density. There is thus a need for new functional binders with facile features compatible with novel electrode materials and chemistries. Here in this review we consider the strategies for rationally designing these functional binders. On the basis of fundamental understandings of the issues for high-energy electrode materials, we have summarized seven desired functions that binders should possess depending on the target electrodes where the binders will be applied. Then a variety of leading-edge functional binders are reviewed to show how their chemical structures realize these above functions and how the employment of these binders affects the cell's electrochemical performances. Finally the corresponding design strategies are therefore proposed, and future research opportunities as well as challenges relating to LBRB binders are outlined.

Adenosine triphosphate (ATP)-binding cassette (ABC) transporters are ubiquitous ATP-dependent membrane proteins involved in translocations of a wide variety of substrates across cellular membranes. To understand the chemomechanical coupling mechanism as well as functional asymmetry in these systems, a quantitative description of how ABC transporters hydrolyze ATP is needed. Complementary to experimental approaches, computer simulations based on combined quantum mechanical and molecular mechanical (QM/MM) potentials have provided new insights into the catalytic mechanism in ABC transporters. Quantitatively reliable determination of the free energy requirement for enzymatic ATP hydrolysis, however, requires substantial statistical sampling on QM/MM potential. A case study shows that brute force sampling of ab initio QM/MM (AI/MM) potential energy surfaces is computationally impractical for enzyme simulations of ABC transporters. On the other hand, existing semiempirical QM/MM (SE/MM) methods, although affordable for free energy sampling, are unreliable for studying ATP hydrolysis. To close this gap, a multiscale QM/MM approach named reaction path–force matching (RP–FM) has been developed. In RP–FM, specific reaction parameters for a selected SE method are optimized against AI reference data along reaction paths by employing the force matching technique. The feasibility of the method is demonstrated for a proton transfer reaction in the gas phase and in solution. The RP–FM method may offer a general tool for simulating complex enzyme systems such as ABC transporters.