Force fields for macromolecular assemblies containing Diketopyrrolopyrrole and Thiophene

Utilizing a force-matching procedure, we parametrize new force fields systematically for large conjugated systems. We model both conjugated polymers and molecular crystals that contain diketopyrrolopyrrole, thiophene, and thieno[3,2-b]thiophene units. These systems have recently been found to have low band gaps, which exhibit high efficiency for photovoltaic devices. The equilibrium structures, forces, and energies of the building block chromophores, diketopyrrolopyrrole, thiophene, and thieno[3,2-b]thiophene computed using our parameters are comparable to those computed using the reference electronic structure method. We assess the suitability of this new force field for electronic property calculations by comparing the electronic excitation properties computed along classical and ab initio molecular dynamics trajectories. For both trajectories, we find similar distributions of TDDFT-calculated excitation energies and oscillator strengths for the building block chromophore diketopyrrolopyrrole-thieno[3,2-b]thiophene. The structural, dynamic, and electronic properties of the macromolecular assemblies built upon these chromophores are characterized. For both polymers and molecular crystals, pronounced peaks around 0° or 180° are observed for the torsions between chromophores under ambient conditions. The high planarity in these systems can promote local ordering and π–π stacking, thereby potentially facilitating charge transport across these materials. For the model conducting polymers, we found that the fluctuations in the density of states per chain per monomer is negligibly small and does not vary significantly with chains comprising 20–40 monomers. Analysis of the electron–hole distributions and the transition density matrices indicates that the delocalized length is approximately 4–6 monomers, which is in good agreement with other theoretical and experimental studies of different conducting polymers. For the molecular crystals, our investigation of the characteristic time scale of the fluctuation in the excitonic couplings shows that a low-frequency vibration below 100 cm–1 is observed for the nearest neighbors. These observations are in line with previous studies on other molecular crystals, in which low-frequency vibrations are believed to be responsible for the large modulation of the excitonic coupling. Thus, our approach and the new force fields provide a direct route for studying the structure–property relations and the molecular level origins of the high efficiency of these classes of materials

The potential for dietary factors to prevent or treat osteoarthritis

Osteoarthritis (OA) is a degenerative joint disease for which there are no disease-modifying drugs. It is a leading cause of disability in the UK. Increasing age and obesity are both major risk factors for OA and the health and economic burden of this disease will increase in the future. Focusing on compounds from the habitual diet that may prevent the onset or slow the progression of OA is a strategy that has been under-investigated to date. An approach that relies on dietary modification is clearly attractive in terms of risk/benefit and more likely to be implementable at the population level. However, before undertaking a full clinical trial to examine potential efficacy, detailed molecular studies are required in order to optimise the design. This review focuses on potential dietary factors that may reduce the risk or progression of OA, including micronutrients, fatty acids, flavonoids and other phytochemicals. It therefore ignores data coming from classical inflammatory arthritides and nutraceuticals such as glucosamine and chondroitin. In conclusion, diet offers a route by which the health of the joint can be protected and OA incidence or progression decreased. In a chronic disease, with risk factors increasing in the population and with no pharmaceutical cure, an understanding of this will be crucial

Micro-computed tomography assisted distal femur metaphyseal blunt punch compression for determining trabecular bone strength in mice

Shorter generation time and the power of genetic manipulation make mice an ideal model system to study bone biology as well as bone diseases. However their small size presents a challenge to perform strength measurements, particularly of the weight-bearing cancellous bone in the murine long bones. We recently developed an improved method to measure the axial compressive strength of the cancellous bone in the distal femur metaphysis in mice. Transverse micro-computed tomography image slices that are 7µm thick were used to locate the position where the epiphysis-metaphysis transition occurs. This enabled the removal of the distal femur epiphysis at the exact transition point exposing the full extent of metaphyseal trabecular bone, allowing more accurate and consistent measurement of its strength. When applied to a murine model system consisting of five month old male wild-type (WT) and Ca(2+)/calmodulin dependent protein kinase kinase 2 (CaMKK2) knockout (KO) Camkk2(-/-) mice that possess recorded differences in trabecular bone volume, data collected using this method showed good correlation between bone volume fraction and strength of trabecular bone. In combination with micro-computed tomography and histology, this method will provide a comprehensive and consistent assessment of the microarchitecture and tissue strength of the cancellous bone in murine mouse models

First principles predictions of thermophysical properties of refrigerant mixtures

We present pair potentials for fluorinated methanes and their dimers with CO2 based on ab initio potential energy surfaces. These potentials reproduce the experimental second virial coefficients of the pure fluorinated methanes and their mixtures with CO2 without adjustment. Ab initio calculations on trimers are used to model the effects of nonadditive dispersion and induction. Simulations using these potentials reproduce the experimental phase-coexistence properties of CH3F within 10% over a wide range of temperatures. The phase coexistence curve of the mixture of CH2F2 and CO2 is reproduced with an error in the mole fractions of both phases of less than 0.1. The potentials described here are based entirely on ab initio calculations, with no empirical fits to improve the agreement with experiment

the origin of the enhanced activity of the π-acceptor phosphinine ligand

The factors governing the activity in Rh-catalyzed hydroformylation were investigated using a set of computational tools. We performed DFT calculations on the phosphinine-modified Rh catalyst [HRh(CO)3(PC5H2R3)] and compared it to the phosphane-modified HRh(CO)3(PR3) and HRh(CO)2(PR3)2 complexes. The π-acceptor phosphinine ligand coordinates preferentially at the equatorial site of the pentacoordinated Rh complex with the heterocycle perpendicular to the equatorial plane, although the ligand freely rotates around the Rh–P bond. The overall energy barrier can be divided into the following contributions: alkene complex formation, alkene rotation and alkene insertion. In the absence of steric effects (model systems), the overall barrier correlates with the computed barrier for alkene rotation. This proves that π-acceptor ligands reduce back-donation to the alkene, leading to a lower rotational barrier and, consequently, to a higher activity. The Rh–P donor–acceptor interactions were quantified using a modified version of energy decomposition analysis (EDA). In Rh–phosphinine systems, the efficient directionality of the π-back-donation, rather than the overall acceptor ability, is responsible for the high catalytic activity. Introducing steric effects increases the energy required to coordinate the alkene, increasing the overall barrier. The factors governing the activity in Rh–monophosphane catalysts seem to be related to those derived for Rh–diphosphane during the development of a QSAR model (Catal. Sci. Technol. 2012, 2, 1694). To investigate whether the findings for mono- can be extrapolated to diphosphane ligands, we re-examined our previous QSAR model using the Topological Maximum Cross Correlation (TMACC) method based on easy-to-interpret 2D-descriptors. The TMACC descriptors highlight heteroatoms close to phosphorus as activity-increasing atoms, whereas highly substituted carbon atom groups are highlighted as activity-decreasing groups

Developing the Saegusa-Ito cyclisation for the synthesis of difluorinated cyclohexenones

Palladium(II)-catalysed cycloalkenylation (Saegusa-Ito cyclisation) has been used for the first time to transform difluorinated silylenol ethers to difluorinated cycloalkenones under mild conditions. The silylenol ether precursors were prepared in two high-yielding steps from trifluoroethanol, and cyclised in moderate to good yields. A combination of air and copper(I) chloride in acetonitrile achieved the turnover of the initial palladium(II) salt, while the provision of an oxygen atmosphere ensured more rapid reaction. Annulations required a minimum level of substitution on the chain, but failed when the alkene was substituted. Annelations allowed a range of n,6-bicyclic systems to be prepared and afforded three products in which heterocycles were fused to the new cyclohexenone. The least substituted system explored underwent cyclisation followed by terminal oxidation to a cyclic enal, which corresponded to a Wacker product of unusual regiochemistry

Birth and Neonatal Transition in the Guinea Pig: Experimental Approaches to Prevent Preterm Birth and Protect the Premature Fetus

The guinea pig (Cavia porcellus) displays many features of gestational physiology that makes it the most translationally relevant rodent species. Progesterone production undergoes a luteal to placental shift as in human pregnancy with levels rising during gestation and with labor and delivery occurring without a precipitous decline in maternal progesterone levels. In contrast to other laboratory rodents, labor in guinea pigs is triggered by a functional progesterone withdrawal, which involves the loss of uterine sensitivity to progesterone like in women. In both species the amnion membrane is a major source of labor-inducing prostaglandins, which promote functional progesterone withdrawal by modifying myometrial progesterone receptor expression. These similar features appear to result from convergent evolution rather than closer evolutionally relationship to primates compared to other rodents. Nevertheless, the similarities in the production, metabolism and actions of progesterone and prostaglandins allow information gained in pregnant guinea pigs to be extended to pregnant women with confidence. This includes exploring the effects of pregnancy complications including growth restriction and the mechanisms by which stressful conditions increase the incidence of preterm labor. The relatively long gestation of the guinea pig and the maturity of the pups at birth particularly in brain development means that a greater proportion of brain development happens in utero. This allows adverse intrauterine conditions to make a sustained impact on the developing brain like in compromised human pregnancies. In addition, the brain is exposed to a protective neurosteroid environment in utero, which has been suggested to promote development in the guinea pig and the human. Moreover, in utero stresses that have been shown to adversely affect long term neurobehavioral outcomes in clinical studies, can be modeled successfully in guinea pigs. Overall, these parallels to the human have led to increasing interest in the guinea pig for translational studies of treatments and therapies that potentially improve outcomes following adverse events in pregnancy and after preterm birth

Effect of Oriented Electric Fields on Biologically Relevant Iron–Sulfur Clusters: Tuning Redox Reactivity for Catalysis

Enzyme-based iron-sulfur clusters, exemplified in families such as hydrogenases, nitrogenases, and radical S-Adenosylmethionine enzymes, feature in many essential biological processes. The functionality of biological iron-sulfur clusters extends beyond simple electron transfer, relying primarily on the redox activity of the clusters, with a remarkable diversity for different enzymes. The active-site structure and the electrostatic environment in which the cluster resides direct this redox reactivity. Oriented electric fields in enzymatic active sites can be significantly strong, and understanding the extent of their effect on iron-sulfur cluster reactivity can inform first steps toward rationally engineering their reactivity. An extensive systematic density functional theory-based screening approach using OPBE/TZP has afforded a simple electric field-effect representation. The results demonstrate that the orientation of an external electric field of strength 28.8 MV cm-1 at the center of the cluster can have a significant effect on its relative stability in the order of 35 kJ mol-1. This shows clear implications for the reactivity of iron-sulfur clusters in enzymes. The results also demonstrate that the orientation of the electric field can alter the most stable broken-symmetry state, which further has implications on the directionality of initiated electron-Transfer reactions. These insights open the path for manipulating the enzymatic redox reactivity of iron-sulfur cluster-containing enzymes by rationally engineering oriented electric fields within the enzymes