Young-Do Won

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous con

Presented are parameters for mono-, di-, and trivalent cations compatible with the CHARMM additive force field and the TIP3P water model. Thermodynamic perturbation molecular dynamics simulations were performed for the cations located at the center of a TIP3P water sphere under a solvent boundary potential. A series of perturbations generated free energies of hydration indexed by the two Lennard-Jones parameters, ε and R(min). Interpolating the experimental free energies of hydration showed that

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSimulation of optical spectra from the reaction center of Rhodopseudomonas viridisYoungdo Won and Richard A. FriesnerCite this: J. Phys. Chem. 1988, 92, 8, 2208–2214Publication Date (Print):April 1, 1988Publication History Published online1 May 2002Published inissue 1 April 1988https://pubs.acs.org/doi/10.1021/j100319a025https://doi.org/10.1021/j100319a025research-articleACS PublicationsRequest reuse permissionsArticle Views121Altmetric-Citations48LEAR

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTheoretical study of photochemical hole burning in photosynthetic bacterial reaction centersYoungdo Won and Richard A. FriesnerCite this: J. Phys. Chem. 1988, 92, 8, 2214–2219Publication Date (Print):April 1, 1988Publication History Published online1 May 2002Published inissue 1 April 1988https://pubs.acs.org/doi/10.1021/j100319a026https://doi.org/10.1021/j100319a026research-articleACS PublicationsRequest reuse permissionsArticle Views63Altmetric-Citati

A remote plasma atomic layer deposition (RPALD) method has been applied to grow a hafnium oxide thin film on the Si substrate. The deposition process was monitored by in situ XPS and the as-deposited structure and chemical bonding were examined by TEM and XPS. The in situ XPS measurement showed the presence of a hafnium silicate phase at the initial stage of the RPALD process up to the 20th cycle and indicated that no hafnium silicide was formed. The initial hafnium silicate was amorphous and gr

An effective Hamiltonian formalism is used to calculate the homogeneous linewidth of long-wavelength absorption in the photosynthetic reaction center. Agreement with the experimental values of approximately 400 cm(-1) for the hole width of the 990-nm band of Rhodopseudomonas viridis is obtained. The anomalously (two orders of magnitude) large width is explained in terms of resonant coupling to charge transfer states. These results support a dynamical model of primary charge separation [Friesner,

Techniques for the calculation of analytic first derivatives of the Hartree–Fock energy are reported, within the context of the pseudospectral ab initio method. Using these gradients, geometry optimization is carried out on several molecules at the 6-31 G** level. The resultant geometries are compared to those from conventional ab initio molecular-orbital calculations, and it is shown that bond lengths agree to within 0.003 Å, while bond angles are within 1°.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTheoretical study of photochemical hole burning in photosynthetic bacterial reaction centers [Erratum to document cited in CA108(19):164946n]Youngdo Won and Richard A. FriesnerCite this: J. Phys. Chem. 1989, 93, 2, 1007Publication Date (Print):January 1, 1989Publication History Published online1 May 2002Published inissue 1 January 1989https://pubs.acs.org/doi/10.1021/j100339a089https://doi.org/10.1021/j100339a089research-articleACS PublicationsRequest

An approximate matrix continued fraction method for calculating optical line shapes of molecular systems with multilevel excited state manifolds is compared with converged basis set results. It is shown that the theory gives correct spectral envelopes for all parameter values studied.

Abstract The temperature dependence of the longwavelength absorption band of the Rhodopseudomonas viridis reaction center is investigated with a thermal expansion model of the special pair. The validity of the model is demonstrated through the reproduction of optical lineshapes measured at various temperatures and through the consistency of the energetic parameters obtained in this fashion. The connection with the temperature dependence of the primary electron transfer process is briefly discuss