Young Min Rhee

Multiplexed-Replica Exchange Molecular Dynamics Method for Protein Folding Simulation

Simulating protein folding thermodynamics starting purely from a protein sequence is a grand challenge of computational biology. Here, we present an algorithm to calculate a canonical distribution from molecular dynamics simulation of protein folding. This algorithm is based on the replica exchange method where the kinetic trapping problem is overcome by exchanging noninteracting replicas simulated at different temperatures. Our algorithm uses multiplexed-replicas with a number of independent molecular dynamics runs at each temperature. Exchanges of configurations between these multiplexed-replicas are also tried, rendering the algorithm applicable to large-scale distributed computing (i.e., highly heterogeneous parallel computers with processors having different computational power). We demonstrate the enhanced sampling of this algorithm by simulating the folding thermodynamics of a 23 amino acid miniprotein. We show that better convergence is achieved compared to constant temperature molecular dynamics simulation, with an efficient scaling to large number of computer processors. Indeed, this enhanced sampling results in (to our knowledge) the first example of a replica exchange algorithm that samples a folded structure starting from a completely unfolded state.

An Improved Algorithm for Analytical Gradient Evaluation in Resolution-of-the-Identity Second-Order Møller-Plesset Perturbation Theory: Application to Alanine Tetrapeptide Conformational Analysis

We present a new algorithm for analytical gradient evaluation in resolution‐of‐the‐identity second‐order Møller‐Plesset perturbation theory (RI‐MP2) and thoroughly assess its computational performance and chemical accuracy. This algorithm addresses the potential I/O bottlenecks associated with disk‐based storage and access of the RI‐MP2 t‐amplitudes by utilizing a semi‐direct batching approach and yields computational speed‐ups of approximately 2–3 over the best conventional MP2 analytical gradient algorithms. In addition, we attempt to provide a straightforward guide to performing reliable and cost‐efficient geometry optimizations at the RI‐MP2 level of theory. By computing relative atomization energies for the G3/99 set and optimizing a test set of 136 equilibrium molecular structures, we demonstrate that satisfactory relative accuracy and significant computational savings can be obtained using Pople‐style atomic orbital basis sets with the existing auxiliary basis expansions for RI‐MP2 computations. We also show that RI‐MP2 geometry optimizations reproduce molecular equilibrium structures with no significant deviations (>0.1 pm) from the predictions of conventional MP2 theory. As a chemical application, we computed the extended‐globular conformational energy gap in alanine tetrapeptide at the extrapolated RI‐MP2/cc‐pV(TQ)Z level as 2.884, 4.414, and 4.994 kcal/mol for structures optimized using the HF, DFT (B3LYP), and RI‐MP2 methodologies and the cc‐pVTZ basis set, respectively. These marked energetic discrepancies originate from differential intramolecular hydrogen bonding present in the globular conformation optimized at these levels of theory and clearly demonstrate the importance of long‐range correlation effects in polypeptide conformational analysis.

Poly-cyclodextrin and poly-paclitaxel nano-assembly for anticancer therapy

Effective anticancer therapy can be achieved by designing a targeted drug-delivery system with high stability during circulation and efficient uptake by the target tumour cancer cells. We report here a novel nano-assembled drug-delivery system, formed by multivalent host-guest interactions between a polymer-cyclodextrin conjugate and a polymer-paclitaxel conjugate. The multivalent inclusion complexes confer high stability to the nano-assembly, which efficiently delivers paclitaxel into the targeted cancer cells via both passive and active targeting mechanisms. The ester linkages between paclitaxel and the polymer backbone permit efficient release of paclitaxel within the cell by degradation. This novel targeted nano-assembly exhibits significant antitumour activity in a mouse tumour model. The strategy established in this study also provides knowledge for the development of advanced anticancer drug delivery.

Characterization of Vinylgold Intermediates: Gold‐Mediated Cyclization of Acetylenic Amides

Vinylgold intermediates involved in various gold-catalyzedreactions are known to undergo proto-deauration in thepresence of a proton source. The unexpected result drew ourattention on the chemistry of vinylgold intermediatesinvolved and thus prompted us to investigate the gold-mediated cyclization in detail with simple substrates, N-(propargyl)benzamides. Described herein is identification ofthe vinylgold(III) intermediates involved and their reactionpathways, all of which expands our present understanding onthe vinylgold intermediates.The treatment of N-(propargyl)benzamide (1) with anequimolar amount of AuCl

Charged polycyclic aromatic hydrocarbon clusters and the galactic extended red emission

The species responsible for the broad extended red emission (ERE), discovered in 1975 and now known to be widespread throughout the Galaxy, still is unidentified. Spanning the range from ≈540 to 900 nm, the ERE is a photoluminescent process associated with a wide variety of different interstellar environments. Over the years, a number of plausible candidates have been suggested, but subsequent observations ruled them out. The objects that present the ERE also emit the infrared features attributed to free polycyclic aromatic hydrocarbon (PAH) molecules, suggesting that closely related materials are plausible ERE carriers. Here, we show that the peculiar spectra and unique properties of closed-shell cationic PAH dimers satisfy the existing observational constraints and suggest that emission from mixtures of charged PAH clusters accounts for much of the ERE. This work provides a view into the structures, stabilities, abundances, and ionization balance of PAH-related species in the emission zones, which, in turn, reflects physical conditions in the emission zones and sheds fundamental light on the nanoscale processes involved in carbon-particle nucleation and growth and carbonaceous dust evolution in the interstellar medium.

Dynamics on the electronically excited state surface of the bioluminescent firefly luciferase-oxyluciferin system.

Dynamics of the firefly luciferase-oxyluciferin complex in its electronic ground and excited states are studied using various theoretical approaches. By mimicking the physiological conditions with realistic models of the chromophore oxyluciferin, the enzyme luciferase, and solvating water molecules and by performing real time simulations with a molecular dynamics technique on the model surfaces, we reveal that the local chromophore-surrounding interaction patterns differ rather severely in the two states. Because of the presence of protein, the solvation dynamics of water around the chromophore is also peculiar and shows widely different time scales on the two terminal oxygen atoms. In addition, simulations of the emission with the quantum-mechanics/molecular-mechanics approach show a close relationship between the emission color variation and the environmental dynamics, mostly through electrostatic effects from the chromophore-surrounding interaction. We also discuss the importance of considering the time scales of the luminescence and the dynamics of the interaction.

All-Atom Semiclassical Dynamics Study of Quantum Coherence in Photosynthetic Fenna–Matthews–Olson Complex

Although photosynthetic pigment-protein complexes are in noisy environments, recent experimental and theoretical results indicate that their excitation energy transfer (EET) can exhibit coherent characteristics for over hundreds of femtoseconds. Despite the almost universal observations of the coherence to some degree, questions still remain regarding the detailed role of the protein and the extent of high-temperature coherence. Here we adopt a theoretical method that incorporates an all-atom description of the photosynthetic complex within a semiclassical framework in order to study EET in the Fenna-Matthews-Olson complex. We observe that the vibrational modes of the chromophore tend to diminish the coherence at the ensemble level, yet much longer-lived coherences may be observed at the single-complex level. We also observe that coherent oscillations in the site populations also commence within tens of femtoseconds even when the system is initially prepared in a non-oscillatory stationary state. We show that the protein acts to maintain the electronic couplings among the system of embedded chromophores. We also investigate the extent to which the proteins electrostatic modulation that disperses the chromophore electronic energies may affect the coherence lifetime. Further, we observe that even though mutation-induced disruptions in the protein structure may change the coupling pattern, a relatively strong level of coupling and associated coherence in the dynamics still remain. Finally, we demonstrate that thermal fluctuations in the chromophore couplings induce some redundancy in the coherent energy-transfer pathway. Our results indicate that a description of both chromophore coupling strengths and their fluctuations is crucial to better understand coherent EET processes in photosynthetic systems.

Potential energy surfaces for polyatomic reactions by interpolation with reaction path weight: CH2OH+→CHO++H2 reaction

An improved algorithm to construct molecular potential energy surfaces for polyatomic reactions is presented. The method uses the energies, gradients, and Hessians, which can be obtained from ab initio quantum chemical calculations. The surface is constructed by interpolating the local quadratic surfaces with reaction path weights. The method is tested with a five-atom reaction system for which an analytic potential energy surface has been reported together with classical trajectory results. An excellent agreement is achieved for energy partitioning in products obtained by trajectory calculation on the original analytic and interpolated surfaces. Reduction of error caused by the use of the reaction path weight is explained.

Quasidegenerate scaled opposite spin second order perturbation corrections to single excitation configuration interaction

Scaled opposite spin (SOS) second order perturbative corrections to single excitation configuration interaction (CIS) are extended to correctly treat quasidegeneracies between excited states. Two viable methods, termed as SOS-CIS(D(0)) and SOS-CIS(D(1)), are defined, implemented, and tested. Each involves one empirical parameter (plus a second for the SOS-MP2 ground state), has computational cost that scales with the fourth power of molecule size, and has storage requirements that are cubic, with only quantities of the rank of single excitations produced and stored during iterations. Tests on a set of low-lying adiabatic valence excitation energies and vertical Rydberg excitations of organic and inorganic molecules show that the empirical parameter can be acceptably transferred from the corresponding nondegenerate perturbation theories without any further fitting. Further tests on higher excited states show that the new methods correctly perform for surface crossings for which nondegenerate approaches fail. Numerical results show that SOS-CIS(D(0)) appears to treat Rydberg excitations in a more balanced way than SOS-CIS(D(1)) and is, therefore, likely to be the preferred approach. It should be useful for exploring excited state geometries, transition structures, and conical intersections for states of medium to large organic molecules that are dominated by single excitations.

Dispersion-Oriented Soft Interaction in a Frustrated Lewis Pair and the Entropic Encouragement Effect in its Formation

The origin of the stability of a frustrated Lewis pair (FLP) tBu(3)P:B(C(6)F(5))(3) is investigated computationally to demonstrate the importance of the dispersion interaction. To this end, the interaction between alkyl-substituted phosphines (Me(3)P and tBu(3)P) and hexafluorobenzene (C(6)F(6)) is first investigated. Driven by the lone-pair to pi-orbital interaction, the binding energy is found to be even larger than usual pi-pi interaction energies between small aromatic compounds. This character, which is inherited to fluorophenyl-substituted B(C(6)F(5))(3) in the FLP, induces large flexibility in the FLP over the molecular surface of B(C(6)F(5))(3). This soft interaction, in turn, causes an entropic stabilization of the FLP formation in comparison with classical Lewis pairs based on close and tight P-B dative bonds. It also suggests a diverse nature of the FLP when it is involved in chemical reactions. Even with the cooperative participation of the perfluorophenyl groups, a detailed inspection of the FLP interaction potential energy surface indicates that the boron atom is still the major interaction site for the pair formation. This non-negligible direct P-B interaction, which is related also to the soft nature of the borane frontier orbital, is further supported by substantial spatial overlap between the frontier orbitals on the phosphine/borane fragments and their interaction energy estimations.