A theoretical insight into the photophysics of psoralen

Psoralen photophysics has been studied on quantum chemistry grounds using the multiconfigurational second-order perturbation method CASPT2. Absorption and emission spectra of the system have been rationalized by computing the energies and properties of the low-lying singlet and triplet excited states. The S1 ππ* state has been determined to be responsible of the lowest absorption and fluorescence bands and to initially carry the population in the photophysical processes related to the phototherapeutic properties of psoralen derivatives. The low-lying T1 ππ* state is, on the other hand, protagonist of the phosphorescence, and its prevalent role in the reactivity of psoralen is suggested to be related to the elongation of the pyrone ring C3–C4 bond, where the spin density is distributed on both carbon atoms. Analysis of energy gaps and spin-orbit coupling elements indicates that the efficient photophysical process leading to the population of the lowest triplet state does not take place at the Franck-Condon region but along the S1 relaxation [email protected] [email protected] [email protected]

Excited states of the water molecule : Analysis of the valence and Rydberg character

The excited states of the water molecule have been analyzed by using the extended quantum-chemical multistate CASPT2 method, namely, MS-CASPT2, in conjunction with large one-electron basis sets of atomic natural orbital type. The study includes 13 singlet and triplet excited states, both valence and 3s-, 3p-, and 3d-members of the Rydberg series converging to the lowest ionization potential and the 3s- and 3p-Rydberg members converging to the second low-lying state of the cation, 1 math. The research has been focused on the analysis of the valence or Rydberg character of the low-lying states. The computation of the 1 math state of water at different geometries indicates that it has a predominant 3s-Rydberg character at the equilibrium geometry of the molecule but it becomes progressively a valence state described mainly by the one-electron 1b1→4a1 promotion, as expected from a textbook of general chemistry, upon elongation of the O–H bonds. The described valence-Rydberg mixing is established to be originated by a molecular orbital (MO) Rydbergization process, as suggested earlier by R. S. Mulliken [Acc. Chem. Res. 9, 7 (1976)] . The same phenomenon occurs also for the 1 math state whereas a more complex behavior has been determined for the 2 math state, where both MO Rydbergization and configurational mixing take place. Similar conclusions have been obtained for the triplet states of the [email protected] [email protected] [email protected]

Ab initio determination of the ionization potentials of DNA and RNA nucleobases

Quantum chemical high level ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute vertical and adiabatic ionization potentials of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. Several states of their cations have been also calculated. The present results represent a systematic compendium of these magnitudes, establishing theoretical reference values at a level not reported before, calibrating computational strategies, and guiding the assignment of the features in the experimental photoelectron [email protected] [email protected] [email protected] [email protected]

Linear and nonlinear optical properties of some organoxenon derivatives

We employ a series of state-of-the-art computational techniques to study the effect of inserting one or more Xe atoms in HC2H and HC4H, on the linear and nonlinear optical (L&NLO) properties of the resulting compounds. It has been found that the inserted Xe has a great effect on the L&NLO properties of the organoxenon derivatives. We analyze the bonding in HXeC2H, and the change of the electronic structure, which is induced by inserting Xe, in order to rationalize the observed extraordinary L&NLO properties. The derivatives, which are of interest in this work, have been synthesized in a Xe matrix. Thus the effect of the local field (LF), due to the Xe environment, on the properties of HXeC2H, has also been computed. It has been found that the LF effect on some properties is significant. The calculations have been performed by employing a hierarchy of basis sets and the techniques MP2 and CCSD(T) for taking into account correlation. For the interpretation of the results we have employed the complete active space valence bond and CASSCF/CASPT2 [email protected]

METADOCK 2: a high-throughput parallel metaheuristic scheme for molecular docking

[EN] Motivation Molecular docking methods are extensively used to predict the interaction between protein-ligand systems in terms of structure and binding affinity, through the optimization of a physics-based scoring function. However, the computational requirements of these simulations grow exponentially with: (i) the global optimization procedure, (ii) the number and degrees of freedom of molecular conformations generated and (iii) the mathematical complexity of the scoring function. Results In this work, we introduce a novel molecular docking method named METADOCK 2, which incorporates several novel features, such as (i) a ligand-dependent blind docking approach that exhaustively scans the whole protein surface to detect novel allosteric sites, (ii) an optimization method to enable the use of a wide branch of metaheuristics and (iii) a heterogeneous implementation based on multicore CPUs and multiple graphics processing units. Two representative scoring functions implemented in METADOCK 2 are extensively evaluated in terms of computational performance and accuracy using several benchmarks (such as the well-known DUD) against AutoDock 4.2 and AutoDock Vina. Results place METADOCK 2 as an efficient and accurate docking methodology able to deal with complex systems where computational demands are staggering and which outperforms both AutoDock Vina and AutoDock 4.This work was partially supported by the Fundación Séneca del Centro de Coordinación de la Investigación de la Región de Murcia [Projects 20813/PI/ 18, 20988/PI/18, 20524/PDC/18] and by the Spanish Ministry of Science, Innovation and Universities [TIN2016-78799-P (AEI/FEDER, UE), CTQ2017-87974-R]. The authors thankfully acknowledge the computer resources at CTE-POWER and the technical support provided by Barcelona Supercomputing Center - Centro Nacional de Supercomputación [RES-BCV2018-3-0008].Imbernón, B.; Serrano, A.; Bueno-Crespo, A.; Abellán, JL.; Pérez-Sánchez, H.; Cecilia-Canales, JM. (2020). METADOCK 2: a high-throughput parallel metaheuristic scheme for molecular docking. Bioinformatics. 1-6. https://doi.org/10.1093/bioinformatics/btz958S16Bianchi, L., Dorigo, M., Gambardella, L. M., & Gutjahr, W. J. (2008). A survey on metaheuristics for stochastic combinatorial optimization. Natural Computing, 8(2), 239-287. doi:10.1007/s11047-008-9098-4Cecilia, J. M., Llanes, A., Abellán, J. L., Gómez-Luna, J., Chang, L.-W., & Hwu, W.-M. W. (2018). High-throughput Ant Colony Optimization on graphics processing units. Journal of Parallel and Distributed Computing, 113, 261-274. doi:10.1016/j.jpdc.2017.12.002Desiraju, G., & Steiner, T. (2001). The Weak Hydrogen Bond. doi:10.1093/acprof:oso/9780198509707.001.0001Eisenberg, D., & McLachlan, A. D. (1986). Solvation energy in protein folding and binding. Nature, 319(6050), 199-203. doi:10.1038/319199a0Ewing, T. J. A., Makino, S., Skillman, A. G., & Kuntz, I. D. (2001). Journal of Computer-Aided Molecular Design, 15(5), 411-428. doi:10.1023/a:1011115820450Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., … Shenkin, P. S. (2004). Glide:  A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy. Journal of Medicinal Chemistry, 47(7), 1739-1749. doi:10.1021/jm0306430Guerrero, G. D., Imbernón, B., Pérez-Sánchez, H., Sanz, F., García, J. M., & Cecilia, J. M. (2014). A Performance/Cost Evaluation for a GPU-Based Drug Discovery Application on Volunteer Computing. BioMed Research International, 2014, 1-8. doi:10.1155/2014/474219Hauser, A. S., & Windshügel, B. (2016). LEADS-PEP: A Benchmark Data Set for Assessment of Peptide Docking Performance. Journal of Chemical Information and Modeling, 56(1), 188-200. doi:10.1021/acs.jcim.5b00234Llanes, A., Muñoz, A., Bueno-Crespo, A., García-Valverde, T., Sánchez, A., Arcas-Túnez, F., … M. Cecilia, J. (2016). Soft Computing Techniques for the Protein Folding Problem on High Performance Computing Architectures. Current Drug Targets, 17(14), 1626-1648. doi:10.2174/1389450117666160201114028McIntosh-Smith, S., Price, J., Sessions, R. B., & Ibarra, A. A. (2014). High performance in silico virtual drug screening on many-core processors. The International Journal of High Performance Computing Applications, 29(2), 119-134. doi:10.1177/1094342014528252Mehler, E. L., & Solmajer, T. (1991). Electrostatic effects in proteins: comparison of dielectric and charge models. «Protein Engineering, Design and Selection», 4(8), 903-910. doi:10.1093/protein/4.8.903Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639-1662. doi:10.1002/(sici)1096-987x(19981115)19:143.0.co;2-bMysinger, M. M., Carchia, M., Irwin, J. J., & Shoichet, B. K. (2012). Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. Journal of Medicinal Chemistry, 55(14), 6582-6594. doi:10.1021/jm300687eO’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1). doi:10.1186/1758-2946-3-33Sakurai, Y., Kolokoltsov, A. A., Chen, C.-C., Tidwell, M. W., Bauta, W. E., Klugbauer, N., … Davey, R. A. (2015). Two-pore channels control Ebola virus host cell entry and are drug targets for disease treatment. Science, 347(6225), 995-998. doi:10.1126/science.1258758Sánchez-Linares, I., Pérez-Sánchez, H., Cecilia, J. M., & García, J. M. (2012). High-Throughput parallel blind Virtual Screening using BINDSURF. BMC Bioinformatics, 13(S14). doi:10.1186/1471-2105-13-s14-s13Sliwoski, G., Kothiwale, S., Meiler, J., & Lowe, E. W. (2013). Computational Methods in Drug Discovery. Pharmacological Reviews, 66(1), 334-395. doi:10.1124/pr.112.007336Sörensen, K. (2013). Metaheuristics-the metaphor exposed. International Transactions in Operational Research, 22(1), 3-18. doi:10.1111/itor.12001Yuan, S., Chan, J. F.-W., den-Haan, H., Chik, K. K.-H., Zhang, A. J., Chan, C. C.-S., … Yuen, K.-Y. (2017). Structure-based discovery of clinically approved drugs as Zika virus NS2B-NS3 protease inhibitors that potently inhibit Zika virus infection in vitro and in vivo. Antiviral Research, 145, 33-43. doi:10.1016/j.antiviral.2017.07.00

Computation of conical intersections by using perturbation techniques

Multiconfigurational second-order perturbation theory, both in its single-state multiconfigurational second-order perturbation theory (CASPT2) and multistate (MS-CASPT2) formulations, is used to search for minima on the crossing seams between different potential energy hypersurfaces of electronic states in several molecular systems. The performance of the procedures is tested and discussed, focusing on the problem of the nonorthogonality of the single-state perturbative solutions. In different cases the obtained structures and energy differences are compared with available complete active space self-consistent field and multireference configuration interaction solutions. Calculations on different state crossings in LiF, formaldehyde, the ethene dimer, and the penta-2,4-dieniminium cation illustrate the discussions. Practical procedures to validate the CASPT2 solutions in polyatomic systems are explored, while it is shown that the application of the MS-CASPT2 procedure is not straightforward and requires a careful analysis of the stability of the results with the quality of the reference wave functions, that is, the size of the active [email protected] [email protected] [email protected]

Context-dependent roles of cellular senescence in normal, aged, and disease states.

Cellular senescence is a state of irreversible cell cycle arrest that often emerges after tissue damage and in age-related diseases. Through the production of a multicomponent secretory phenotype (SASP), senescent cells can impact the regeneration and function of tissues. However, the effects of senescent cells and their SASP are very heterogeneous and depend on the tissue environment and type as well as the duration of injury, the degree of persistence of senescent cells and the organism's age. While the transient presence of senescent cells is widely believed to be beneficial, recent data suggest that it is detrimental for tissue regeneration after acute damage. Furthermore, although senescent cell persistence is typically associated with the progression of age-related chronic degenerative diseases, it now appears to be also necessary for correct tissue function in the elderly. Here, we discuss what is currently known about the roles of senescent cells and their SASP in tissue regeneration in ageing and age-related diseases, highlighting their (negative and/or positive) contributions. We provide insight for future research, including the possibility of senolytic-based therapies and cellular reprogramming, with aims ranging from enhancing tissue repair to extending a healthy lifespan.Work in the authors’ laboratory is supported by MINECO-Spain (RTI2018-096068), H2020 European Research Council-2016-AdG-741966, LaCaixaHEALTH-HR17-00040, MWRF, French Muscular Dystrophy Association, Muscular Dystrophy Association, Fundacio LaMarató TV3 (80/19-202021 and 137/ 38-202033) and UPGRADE-H2020-825825; and María-de-Maeztu-Program for Units of Excellence to UPF (MDM-2014-0370), Severo Ochoa-Program for Centers of Excellence to CNIC (SEV-2015-0505).S

Effects of Extending Milk Replacer Feeding during the Fattening Period on the Behaviour and Welfare of Lambs: A Preliminary Study

There is a lack of information on the behavioural and welfare effects of sustaining artificial milk feeding in fattening lambs. Therefore, the present work aimed to study the effects of prolonged artificial milk feeding during fattening with a high concentrate diet on the behaviour of lambs. The behaviour of 16 non castrated male lambs of the Manchega sheep breed (eight lambs were in the group that were fed daily a bottle of milk, and the other eight were in the weaned group) was recorded with four fixed cameras just before bottle feeding (~8:30 a.m.) of the unweaned group till four hours later, every day for 7 weeks. The solid diet (pelleted concentrate plus cereal straw) and housing conditions were the same in both groups. Solid feeds were offered ad libitum. There were no differences between groups in time spent eating nor in drinking, playing, scratching and oral activity behaviours (p > 0.05), but resting episodes were longer in weaned lambs (p < 0.05). Weaned lambs presented a higher frequency of self-grooming behaviour (p < 0.05), while the unweaned group performed a higher frequency of interaction behaviour (p < 0.05). In conclusion, the behaviours of lambs that were fed daily a bottle of milk during the fattening period did not substantially differ from the weaned individuals

Effectiveness of gold nanorods of different sizes in photothermal therapy to eliminate melanoma and glioblastoma cells

Gold nanorods are the most commonly used nanoparticle in photothermal therapy (PTT) due to their efficiency to convert the light into heat. This study aimed to investigate the efficacy of gold nanorods of different sizes (large and small) in eliminating two types of cancer cells: glioblastoma and melanoma cells. After the cytotoxic profiles of the nanoparticles were stablished, PTT was applied to the melanoma and glioblastoma cells with a high efficiency and mortality rate. Several methods were used to evaluate the efficiency of PTT including fluorescence, confocal or dark field microscopy, biochemical analysis, and flow cytometry. To determine cell viability and the type of cell death triggered by PTT, Calcein-propidium iodide, Annexin-V staining and dehydrogenase activity assays were performed. Our findings revealed that after PTT was applied to the cancer cells, the main cell death was apoptosis. This is advantageous as the presence of apoptotic cells can stimulate antitumoral immunity in vivo. Considering the high efficacy of these gold nanorods in PTT, large nanoparticles could be useful for biofunctionalization purposes. Large nanorods offer a greater surface area for attaching biomolecules, thereby promoting high sensitivity and specificity in recognizing target cancer cells. Additionally, large nanoparticles could also be beneficial for theragnostic applications, involving both therapy and diagnosis, due to their superior detection sensitivity

Effectiveness of gold nanorods of different sizes in photothermal therapy to eliminate melanoma and glioblastoma cells

Gold nanorods are the most commonly used nanoparticle in photothermal therapy (PTT) due to their efficiency to convert the light into heat. This study aimed to investigate the efficacy of gold nanorods of different sizes (large and small) in eliminating two types of cancer cells: glioblastoma and melanoma cells. After the cytotoxic profiles of the nanoparticles were stablished, PTT was applied to the melanoma and glioblastoma cells with a high efficiency and mortality rate. Several methods were used to evaluate the efficiency of PTT including fluorescence, confocal or dark field microscopy, biochemical analysis, and flow cytometry. To determine cell viability and the type of cell death triggered by PTT, Calcein-propidium iodide, Annexin-V staining and dehydrogenase activity assays were performed. Our findings revealed that after PTT was applied to the cancer cells, the main cell death was apoptosis. This is advantageous as the presence of apoptotic cells can stimulate antitumoral immunity in vivo. Considering the high efficacy of these gold nanorods in PTT, large nanoparticles could be useful for biofunctionalization purposes. Large nanorods offer a greater surface area for attaching biomolecules, thereby promoting high sensitivity and specificity in recognizing target cancer cells. Additionally, large nanoparticles could also be beneficial for theragnostic applications, involving both therapy and diagnosis, due to their superior detection sensitivity