Turro, N. J., Ramamurthy, V., & Scaiano, J. C. (2010). Modern molecular photochemistry of organic molecules. University Science Books.
Klan, P., & Wirz, J. (2009). Photochemistry of organic compounds. John Wiley & Sons Ltd.
Photochemistry in Organized and Constrained Media, V. Ramamurthy (Ed.), VCH Publishers, New York, 1991.
Supramolecular Photochemistry, V. Ramamurthy & Y. Inoue (Eds.), John Wiley, Hoboken, 2011.
Supramolecular Photochemistry, V. Balzani & F. Scandola (Eds.), Ellis Horwood, Chichester, UK, 1991.
Frontiers in Supramolecular Organic Chemistry and Photochemistry, H.-J. Schneider & H. Durr (Eds.),VCH, New York, 1991.
V. Ramamurthy, R.G. Weiss & G.S. Hammond, A Model for the Influence of Organized Media on Photochemical Reactions, Advances in Photochemistry, Vol. 18, John Wiley & Sons, Inc., 1993. pp. 67–234.
Weiss, R. G., Ramamurthy, V., & Hammond, G. S. (1993). Photochemistry in organized and confining media: a model. Accounts of Chemical Research, 26, 530–536.
G.M.J. Schmidt,The photochemistry of the solid state, Reactivity of the photoexcited organic molecule, Proceedings of the Thirteenth Conference on Chemistry at the University of Brussels, October 1965, John Wiley, New York, 1967, 227–288.
Ramamurthy, V., & Sivaguru, J. (2016). Supramolecular photochemistry as a synthetic tool: photocycloaddition. Chemical Reviews, 116, 9914–9993.
Article CAS PubMed Google Scholar
Ramamurthy, V., & Venkatesan, K. (1987). Photochemical reactions of organic crystals. Chemical Reviews, 87, 433–481.
G. M. J. Schmidt et al. Solid State Photochemistry, D. Ginsburg ((Ed.), Verlag Chemie, Weinheim, 1976.
Cohen, M. D. (1975). The photochemistry of organic solids. Angewandte Chemie (International ed. in English), 14, 386–393.
G.M.J. Schmidt, (1964), Topochemistry. III. The crystal chemistry of some trans-cinnamic acids, J. Chem. Soc., 2014–2021.
Gibb, C. L. D., & Gibb, B. C. (2004). Well-defined, organic nanoenvironments in water: the hydrophobic effect drives capsular assembly. Journal of the American Chemical Society, 126, 11408–11409.
Article CAS PubMed Google Scholar
Choudhury, R., Barman, A., Prabhakar, R., & Ramamurthy, V. (2013). Hydrocarbons depending on the chain length and head group adopt different conformations within a water-soluble nanocapsule: 1H NMR and molecular dynamics studies. The Journal of Physical Chemistry B, 117, 398–407.
Article CAS PubMed Google Scholar
Kulasekharan, R., Choudhury, R., Prabhakara, R., & Ramamurthy, V. (2011). Restricted rotation due to the lack of free space within a capsule translates into product selectivity: Photochemistry of cyclohexyl phenyl ketones within a water-soluble organic capsule. Chemical Communications, 47, 2841–2843.
Article CAS PubMed Google Scholar
Ramkumar Varadharajan, Sarah Ariel Kelley, Vindi M. Jayasinghe-Arachchige, Rajeev Prabhakar, V. Ramamurthy & S.C. Blackstock, (2022), Organic Host Encapsulation Effects on Nitrosobenzene Monomer−Dimer Distribution and C−NO Bond Rotation in an Aqueous Solution, ACS Org. Inorg. Au, 2, 175-185
A.H. Elcock, D. Sept & J.A. McCammon, (2001), Computer Simulation of Protein−Protein Interactions, J. Phys. Chem., B, 105, 1504–1518.
Baaden, M., & Marrink, S. J. (2013). Coarse-grain modelling of protein–protein interactions. Current Opinion in Structural Biology, 23, 878–886.
Article CAS PubMed Google Scholar
Basdevant, N., Weinstein, H., & Ceruso, M. (2006). Thermodynamic basis for promiscuity and selectivity in protein−protein interactions: PDZ domains, a case study. Journal of the American Chemical Society, 128, 12766–12777.
Article CAS PubMed PubMed Central Google Scholar
Salsbury, F. R. (2010). Molecular dynamics simulations of protein dynamics and their relevance to drug discovery. Current Opinion in Pharmacology, 10, 738–744.
Article CAS PubMed PubMed Central Google Scholar
Friedman, R. (2022). Computational studies of protein–drug binding affinity changes upon mutations in the drug target. WIREs Computational Molecular Science, 12, e1563.
Ozbil, M., Barman, A., Bora, R. P., & Prabhakar, R. (2012). Computational insights into dynamics of protein aggregation and enzyme-substrate interactions. J. Pjys. Chem. Lett., 3, 3460–3469.
Díaz, N., Sordo, T. L., Merz, K. M., & Suárez, D. (2003). Insights into the acylation mechanism of class A β-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin. Journal of the American Chemical Society, 125, 672–684.
Sharma, G., Hu, Q., Jayasinghe-Arachchige, V. M., Paul, T. J., Schenk, G., & Prabhakar, R. (2019). Investigating coordination flexibility of glycerophosphodiesterase (GpdQ) through interactions with mono-, di-, and triphosphoester (NPP, BNPP, GPE, and paraoxon) substrates. Physical Chemistry Chemical Physics: PCCP, 21, 5499–5509.
Article CAS PubMed Google Scholar
Cisneros, G. A., Karttunen, M., Ren, P., & Sagui, C. (2014). Classical electrostatics for biomolecular simulations. Chemical Reviews, 114, 779–814.
Article CAS PubMed Google Scholar
R. Kapral & G. Ciccotti,Chapter 16 - Molecular dynamics: An account of its evolution, C.E. Dykstra, G. Frenking, K.S. Kim, G.E. Scuseria (Eds.) Theory and Applications of Computational Chemistry, Elsevier, Amsterdam, 2005, 425–441.
Rahman, A., & Stillinger, F. H. (2003). Molecular dynamics study of liquid water. The Journal of Chemical Physics, 55, 3336–3359.
H.J.C. Berendsen, Molecular dynamics simulations: The limits and beyond, Springer, 1999.
Pokorna, P., Kruse, H., Krepl, M., & Sponer, J. (2018). QM/MM calculations on protein–RNA complexes: Understanding limitations of classical MD simulations and search for reliable cost-effective QM methods. Journal of Chemical Theory and Computation, 14, 5419–5433.
Article CAS PubMed Google Scholar
Gibb, C. L. D., Sundaresan, A. K., Ramamurthy, V., & Gibb, B. C. (2008). Templation of the excited-state chemistry of α-(n-Alkyl) Dibenzyl ketones: How guest packing within a nanoscale supramolecular capsule influences photochemistry. Journal of the American Chemical Society, 130, 4069–4080.
Article CAS PubMed Google Scholar
Das, A., Danao, A., Banerjee, S., Raj, A. M., Sharma, G., Prabhakar, R., Srinivasan, V., Ramamurthy, V., & Sen, P. (2021). Dynamics of anthracene excimer formation within a water-soluble nanocavity at room temperature. Journal of the American Chemical Society, 143, 2025–2036.
Article CAS PubMed Google Scholar
Boeije, Y., & Olivucci, M. (2023). From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions. Chemical Society Reviews, 52, 2643–2687.
Article CAS PubMed Google Scholar
Zhu, T., & Van Voorhis, T. (2016). Charge recombination in phosphorescent organic light-emitting diode host–guest systems through qm/mm simulations. Journal of Physical Chemistry C, 120, 19987–19994.
M. Olsson, A. & U. Ryde, (2017), Comparison of QM/MM Methods to Obtain Ligand-Binding Free Energies, J. Chem. Theory Comput., 13, 2245-2253
Wang, M., Mei, Y., & Ryde, U. (2019). Host–guest relative binding affinities at density-functional theory level from semiempirical molecular dynamics simulations. Journal of Chemical Theory and Computation, 15, 2659–2671.
Article CAS PubMed Google Scholar
Wang, M., Mei, Y., & Ryde, U. (2018). Predicting relative binding affinity using nonequilibrium QM/MM simulations. Journal of Chemical Theory and Computation, 14, 6613–6622.
Article CAS PubMed Google Scholar
Steinmann, C., Olsson, M. A., & Ryde, U. (2018). Relative ligand-binding free energies calculated from multiple short QM/MM MD simulations. Journal of Chemical Theory and Computation, 14, 3228–3237.
Article CAS PubMed Google Scholar
Caldararu, O., Olsson, M. A., Misini Ignjatović, M., Wang, M., & Ryde, U. (2018). Binding free energies in the SAMPL6 octa-acid host–guest challenge calculated with MM and QM methods. Journal of Computer-Aided Molecular Design, 32, 1027–1046.
Article CAS PubMed Google Scholar
Caldararu, O., Olsson, M. A., Riplinger, C., Neese, F., & Ryde, U. (2017). Binding free energies in the SAMPL5 octa-acid host–guest challenge calculated with DFT-D3 and CCSD (T). Journal of Computer-Aided Molecular Design, 31, 87–106.
Article CAS PubMed Google Scholar
Olsson, M. A., Söderhjelm, P., & Ryde, U. (2016). Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level. Journal of Computational Chemistry, 37, 1589–1600.
Article CAS PubMed PubMed Central Google Scholar
Mikulskis, P., Cioloboc, D., Andrejić, M., Khare, S., Brorsson, J., Genheden, S., Mata, R. A., Söderhjelm, P., & Ryde, U. (2014). Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies. Journal of Computer-Aided Molecular Design, 28, 375–400.
Article CAS PubMed Google Scholar
Andrejić, M., Ryde, U., Mata, R. A., & Söderhjelm, P. (2014). Coupled-cluster interaction energies for 200-atom host-guest systems. ChemPhysChem, 15, 3270–3281.
Jing, Z., Liu, C., Cheng, S. Y., Qi, R., Walker, B. D., Piquemal, J.-P., & Ren, P. (2019). Polarizable force fields for biomolecular simulations: recent advances and applications. Ann. Rev. Biophys., 48, 371–394.
Nakata, H., & Bai, S. (2019). Development of a new parameter optimization scheme for a reactive force field based on a machine learning approach. J. Comp. Chem., 40, 2000–2012.
He, X., Man, V. H., Yang, W., Lee, T.-S., & Wang, J. (2020). A fast and high-quality charge model for the next generation general AMBER force field. The Journal of Chemical Physics, 153, 114502.
Article CAS PubMed PubMed Central Google Scholar
Grimme, S. (2019). Exploration of chemical compound, conformer, and reaction space with meta-dynamics simulations based on tight-binding quantum chemical calculations. Journal of Chemical Theory and Computation, 15, 2847–2862.
Article CAS PubMed Google Scholar
Kulasekharan, R., Choudhury, R., Prabhakar, R., & Ramamurthy, V. (2011). Restricted
Comments (0)