| 1. |
Junichi Ono, Yoshihiro Matsumura, Toshifumi Mori, Shinji Saito, Conformational Dynamics in Proteins: Entangled Slow Fluctuations and Nonequilibrium Reaction Events, The Journal of Physical Chemistry B, 10.1021/acs.jpcb.3c05307, 2023.12. |
| 2. |
Akira Shiozuka, Di Wu, Kyohei Kawashima, Toshifumi Mori, Kohei Sekine, Yoichiro Kuninobu, Carbamoylarylation of Alkenes with N-Aryl Oxamic Acids Involving 1,4-Aryl Migration Via C(aryl)–N Bond Cleavage, ACS Catalysis, 10.1021/acscatal.4c00523, 2024.04. |
| 3. |
Toshifumi Mori, Norio Yoshida, Tuning the ATP–ATP and ATP–disordered protein interactions in high ATP concentration by altering water models, The Journal of Chemical Physics, 10.1063/5.0158046, 2023.07.  |
| 4. |
Sirin Sittiwanichai, Deanpen Japrung, Toshifumi Mori, Prapasiri Pongprayoon, Structural and Dynamic Alteration of Glycated Human Serum Albumin in Schiff Base and Amadori Adducts: A Molecular Simulation Study, The Journal of Physical Chemistry B, 10.1021/acs.jpcb.3c02048, 2023.06. |
| 5. |
Di Wu, Akira Shiozuka, Kyohei Kawashima, Toshifumi Mori, Kohei Sekine, Yoichiro Kuninobu, Bifunctional 1-Hydroxypyrene Photocatalyst for Hydrodesulfurization via Reductive C(Aryl)–S Bond Cleavage, Organic Letters, 10.1021/acs.orglett.3c01061, 25, 18, 3293-3297, 2023.05, We developed the visible-light-induced hydrodesulfurization of alkyl aryl thioethers via the reductive cleavage of the C(aryl)-S bond using 1-hydroxypyrene as a Brønsted acid-reductant bifunctional photocatalyst. The hydrodesulfurization reaction proceeded under simple reaction conditions (1-hydroxypyrene and Et3N in THF under purple LED illumination); this reaction did not require chemicals commonly used for hydrodesulfurization, such as hydrosilanes, transition metal catalysts, and/or stoichiometric amounts of metal reagents. Detailed mechanistic studies based on control experiments, spectroscopic measurements, and computational studies revealed that the cleavage of the C(aryl)-S bond and the formation of the C(aryl)-H bond proceeded via the formation of the ion pair between the radical anion of alkyl aryl thioether and Et3N+H, resulting in the generation of a sulfur radical. In addition, the 1-hydroxypyrene catalyst was regenerated via hydrogen atom transfer (HAT) from Et3N.. |
| 6. |
Toshiaki Mori, Kohei Sekine, Kyohei Kawashima, Toshifumi Mori, Yoichiro Kuninobu, Near‐Infrared and Dual Emissions of Diphenylamino Group‐Substituted Malachite Green Derivatives, European Journal of Organic Chemistry, 10.1002/ejoc.202200873, 2022.08. |
| 7. |
Toshifumi Mori, Shinji Saito, Molecular Insights into the Intrinsic Dynamics and Their Roles During Catalysis in Pin1 Peptidyl-prolyl Isomerase, The Journal of Physical Chemistry B, 10.1021/acs.jpcb.2c02095, 126, 5185-5193, 2022.07. |
| 8. |
Akira Shiozuka, Kohei Sekine, Takumi Toki, Kyohei Kawashima, Toshifumi Mori, Yoichiro Kuninobu, Photoinduced Divergent Deaminative Borylation and Hydrodeamination of Primary Aromatic Amines, Organic Letters, 10.1021/acs.orglett.2c01663, 2022.06. |
| 9. |
Takuma Kikutsuji, Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi, Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI), The Journal of Chemical Physics, 10.1063/5.0087310, 156, 15, 154108-154108, 2022.04. |
| 10. |
Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi, Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide, JOURNAL OF CHEMICAL PHYSICS, 10.1063/5.0009066, 153, 5, 2020.08, We propose a cross-entropy minimization method for finding the reaction coordinate from a large number of collective variables in complex molecular systems. This method is an extension of the likelihood maximization approach describing the committor function with a sigmoid. By design, the reaction coordinate as a function of various collective variables is optimized such that the distribution of the committor pB* values generated from molecular dynamics simulations can be described in a sigmoidal manner. We also introduce the L-2-norm regularization used in the machine learning field to prevent overfitting when the number of considered collective variables is large. The current method is applied to study the isomerization of alanine dipeptide in vacuum, where 45 dihedral angles are used as candidate variables. The regularization parameter is determined by cross-validation using training and test datasets. It is demonstrated that the optimal reaction coordinate involves important dihedral angles, which are consistent with the previously reported results. Furthermore, the points with pB*similar to 0.5 clearly indicate a separatrix distinguishing reactant and product states on the potential of mean force using the extracted dihedral angles.. |
| 11. |
Toshifumi Mori, Shinji Saito, Dissecting the Dynamics during Enzyme Catalysis: A Case Study of Pin1 Peptidyl-Prolyl Isomerase, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10.1021/acs.jctc.9b01279, 16, 5, 3396-3407, 2020.05, Free energy surfaces have played a central role in studying protein conformational changes and enzymatic reactions over decades. Yet, free energy barriers and kinetics are highly dependent on the coordinates chosen to define the surface, and furthermore, the dynamics during the reactions are often overlooked. Our recent study on the Pin1-catalyzed isomerization reaction has indicated that the isomerization transition events remarkably deviate from the free energy path, highlighting the need to understand the reaction dynamics in more detail. To this end, here we investigate the reaction coordinates that describe the transition states of the free energy and transition pathways by minimizing the cross-entropy function. We show that the at isomerization transition events can be expressed by the concerted changes in the improper torsion angle and nearby backbone torsional angles of the ligand, whereas the transition state of the free energy surface involves changes in a broad range of coordinates including multiple protein-ligand interactions. The current result supports the previous finding that the isomerization transitions occur quickly from the conformational excited states, which is in sharp contrast to the slow and collective changes suggested from the free energy path. Our results further indicate that the coordinates derived from the transition trajectories are not sufficient for finding the transition states on the free energy surfaces due to the lack of information from conformational excited states.. |
| 12. |
Toshifumi Mori, Shinji Saito, Conformational Excitation and Nonequilibrium Transition Facilitate Enzymatic Reactions: Application to Pin1 Peptidyl-Prolyl Isomerase, JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 10.1021/acs.jpclett.8b03607, 10, 3, 474-480, 2019.02. |
| 13. |
William J. Glover, Toshifumi Mori, Michael S. Schuurman, Andrey E. Boguslavskiy, Oliver Schalk, Albert Stolow, Todd J. Martínez, Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. II. Ab initio multiple spawning simulations, Journal of Chemical Physics, 10.1063/1.5018130, 148, 16, 164303, 2018.04, The excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene (BD), has long been the subject of controversy due to its strong coupling, ultrafast time scales and the difficulties that theory faces in describing the relevant electronic states in a balanced fashion. Here we apply Ab Initio Multiple Spawning (AIMS) using state-averaged complete active space multistate second order perturbation theory [SA-3-CAS(4/4)-MSPT2] which describes both static and dynamic electron correlation effects, providing a balanced description of both the initially prepared bright 11Bu (ππ) state and non-adiabatically coupled dark 21Ag state of BD. Importantly, AIMS allows for on-the-fly calculations of experimental observables. We validate our approach by directly simulating the time resolved photoelectron-photoion coincidence spectroscopy results presented in Paper I [A. E. Boguslavskiy et al., J. Chem. Phys. 148, 164302 (2018)], demonstrating excellent agreement with experiment. Our simulations reveal that the initial excitation to the 11Bu state rapidly evolves via wavepacket dynamics that follow both bright- and dark-state pathways as well as mixtures of these. In order to test the sensitivity of the AIMS results to the relative ordering of states, we considered two hypothetical scenarios biased toward either the bright 1Bu or the dark 21Ag state. In contrast with AIMS/SA-3-CAS(4/4)-MSPT2 simulations, neither of these scenarios yields favorable agreement with experiment. Thus, we conclude that the excited state non-adiabatic dynamics in BD involves both of these ultrafast pathways.. |
| 14. |
Boguslavskiy AE, Schalk O, Gador N, Glover WJ, Mori T, Schultz T, Schuurman MS, Martínez TJ, Stolow A, Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. I. Time-resolved photoelectron-photoion coincidence spectroscopy., The Journal of chemical physics, 10.1063/1.5016452, 148, 16, 164302, 2018.04. |
| 15. |
Mahroof Kalathingal, Takashi Sumikama, Toshifumi Mori, Shigetoshi Oiki, Shinji Saito, Structure and dynamics of solvent molecules inside the polytheonamide B channel in different environments: A molecular dynamics study, Physical Chemistry Chemical Physics, 10.1039/c7cp06299k, 20, 5, 3334-3348, 2018.02, The β6.3-helical channel of the marine cytotoxic peptide, polytheonamide B (pTB), is examined in water, the POPC bilayer, and a 1:1 chloroform/methanol mixture using all-atom molecular dynamics simulations. The structures and fluctuations of the β6.3-helix of pTB are investigated in the three environments. The average structure of pTB calculated in the mixed solvent is in good agreement with the NMR-resolved structure in the mixed solvent, indicating the validity of the parameters used for the non-standard groups in pTB. The configuration and dynamics of solvent molecules inside the pore are examined in detail. It is found that the motions of methanol molecules inside the pore are not correlated because of the absence of strong hydrogen bonds (HBs) between adjacent methanol molecules. On the other hand, the motions of water molecules inside the pore are highly correlated, both translationally and orientationally, due to the strong HBs between neighboring water molecules. It is suggested that the collective behavior of water molecules inside the pore in the membrane is crucial for the permeation of ions through the pTB channel.. |
| 16. |
Prapasiri Pongprayoon, Toshifumi Mori, The critical role of dimer formation in monosaccharides binding to human serum albumin, Physical Chemistry Chemical Physics, 10.1039/c7cp06324e, 20, 5, 3249-3257, 2018.02, Human serum albumin (HSA) is the most abundant transport protein found in human blood. HSA is known to bind a wide range of drugs and monosaccharides, but where and how these molecules bind are largely unknown. Recently, a crystal structure of glycated HSA has been reported, and interestingly, in that structure two glucose molecules have been located in pyranose (GLC) and open chain (GLO) forms bound in the same binding pocket (Sudlow site I). Molecular simulations also proposed two binding modes of GLC and GLO (binding two ligands either in a distant location or in close contact). Yet, how HSA binds sugars in general is poorly understood. To this end, here we study the mechanism of binding glucose and its epimer galactose to HSA using alchemical free energy perturbation calculations and molecular dynamics simulations, and show why two sugar molecules appear in the bound state. We find that HSA does prefer glucose over galactose, in line with experiments, by binding glucose deeper in the pocket. Furthermore, out of the two possible binding modes suggested previously, the binding becomes tighter when the two sugars are in contact
this is achieved by a hydrogen bond connecting the two sugars and filling the large cavity of Sudlow site I as a dimer. We also find tight hydrogen bonds between open chain glucose/galactose and HSA, which includes the possible glycation site K199, while the pyranose form does not interact strongly with any characteristic residues. Thus the current result highlights the importance of dimeric structures of glucose/galactose for binding to HSA and triggering glycation/galactation.. |
| 17. |
Toshifumi Mori, Shinji Saito, Molecular Mechanism Behind the Fast Folding/Unfolding Transitions of Villin Headpiece Subdomain: Hierarchy and Heterogeneity, JOURNAL OF PHYSICAL CHEMISTRY B, 10.1021/acs.jpcb.6b08066, 120, 45, 11683-11691, 2016.11, Proteins involve motions over a wide range of spatial and temporal scales. While the large conformational changes, such as folding and functioning, are slow and appear to occur in a highly cooperative manner, how the hierarchical dynamics over different time scales play a role during these slow transitions has been of great interest over the decades. Here we study the folding mechanism of the villin headpiece subdomain (HP35) to understand the molecular mechanism behind this prototypical fast-folding protein. The similar to 400 mu s molecular dynamics (MD) trajectories obtained by Piana et al. [Piana, S.; Lindorff-Larsen, K.; Shaw, D. E. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 17845] are analyzed in detail. By extracting the slowest mode from the trajectories, which is responsible for the folding/unfolding transitions, and by analyzing the transition events along this mode, we find that the transitions occur in a heterogeneous manner. Detailed analysis of the individual transition events shows that the folding/unfolding transitions occur via two qualitatively different pathways, i.e., the unfolding triggered from the C-terminal (alpha(3) helix) and from the N-terminal (alpha(1)-alpha(2) loop). Non-native contacts are also found to contribute in slowing down the transitions. The folding of HP35 thus proceeds in a segmental manner rather than cooperatively at the submicrosecond time scale. The Lys -> Nle mutation is found to speed up the transitions by rigidifying the alpha(3) helix, i.e., suppressing one transition pathway. The analysis of the microsecond dynamics in the single-molecule Forster resonance energy transfer efficiency trajectories, which are calculated from the MD data, reveals that the folding/unfolding transitions in the NleNle mutant can be fitted with a two-state model, whereas those in WT appear to be more complex and involves multiple time scales. This is due to the coupling between the folding/unfolding transitions and conformational transitions within the unfolded and. intermediate states. The present study demonstrates that a protein as small as HP35 already involves heterogeneous characters during folding/unfolding transitions when the hierarchical dynamics at the molecular level is considered, thus heterogeneity can be a general characteristic in protein folding.. |
| 18. |
Shinji Aono, Toshifumi Mori, Shigeyoshi Sakaki, 3D-RISM-MP2 Approach to Hydration Structure of Pt(II) and Pd(II) Complexes: Unusual H-Ahead Mode vs Usual O-Ahead One, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10.1021/acs.jctc.5b01137, 12, 3, 1189-1206, 2016.03, Solvation of transition metal complexes with water has been one of the fundamental topics in physical and coordination chemistry. In particular, Pt(II) complexes have recently attracted considerable interest for their relation to anticancer activity in cisplatin and its analogues, yet the interaction of the water molecule and the metal center has been obscured. The challenge from a theoretical perspective remains that both the microscopic solvation effect and the dynamical electron correlation (DEC) effect have to be treated simultaneously in a-reasonable manner. In this work we derive the analytical gradient for the three-dimensional reference interaction site model Moller-Plesset second order (3D-RISM-MP2) free energy. On the basis of the three-regions 3D-RISM self-consistent field (SCF) method recently proposed by us, we apply a new layer of the Z-vector method to the CP-RISM equation as well as point-charge approximation to the derivatives with respect to the density matrix elements in the RISM-CPHF equation to remarkably reduce the computational cost. This method is applied to study the interaction of H2O with the d(8) square planar transition metal complexes in aqueous solution, trans[(PtCl2)-Cl-II(NH3)(glycine)] (1a), [Pt-II(NH3)(4)](2+) (1b), [Pt-II(CN)(4)](2-) (1c), and their Pd(II) analogues 2a, 2b, and 2c, respectively, to elucidate whether the usual H2O interaction through O atom (O-ahead mode) or unusual one through H atom (H-ahead mode) is stable in these complexes. We find that the interaction energy of the coordinating water and the, transition metal complex changes little when switching from gas to aqueous phase, but the solvation free energy differs remarkably between the two interaction modes, thereby affecting the relative stability of the H-ahead and O-ahead modes. Particularly, in contrast to the expectation that the O-ahead mode is preferred due to the presence of positive charges in 1b, the H-ahead mode is also found to be more stable. The O-ahead mode is found to be more stable than the H-ahead one only in 2b. The energy decomposition analysis (EDA) at the 3D-RISM-MP2 level revealed that the O-ahead mode is stabilized by the electrostatic (ES) interaction, whereas the H-ahead one is mainly stabilized by the DEC effect. The ES interaction is also responsible for the difference between the Pd(II) and Pt(11) complexes; because the electrostatic potential is more negative along the z-axis in the Pt(II) complex than in the Pd(II) one, the O-ahead mode prefers the Pd(II) complexes, whereas the H-ahead becomes predominant in the Pt(II) complexes.. |
| 19. |
Jun Abe, Takuya B. Hiyama, Atsushi Mukaiyama, Seyoung Son, Toshifumi Mori, Shinji Saito, Masato Osako, Julie Wolanin, Eiki Yamashita, Takao Kondo, Shuji Akiyama, Atomic-scale origins of slowness in the cyanobacterial circadian clock, SCIENCE, 10.1126/science.1261040, 349, 6245, 312-316, 2015.07, Circadian clocks generate slow and ordered cellular dynamics but consist of fast-moving bio-macromolecules; consequently, the origins of the overall slowness remain unclear. We identified the adenosine triphosphate (ATP) catalytic region [adenosine triphosphatase (ATPase)] in the amino-terminal half of the clock protein KaiC as the minimal pacemaker that controls the in vivo frequency of the cyanobacterial clock. Crystal structures of the ATPase revealed that the slowness of this ATPase arises from sequestration of a lytic water molecule in an unfavorable position and coupling of ATP hydrolysis to a peptide isomerization with high activation energy. The slow ATPase is coupled with another ATPase catalyzing autodephosphorylation in the carboxyl-terminal half of KaiC, yielding the circadian response frequency of intermolecular interactions with other clock-related proteins that influences the transcription and translation cycle.. |
| 20. |
Toshifumi Mori, Shinji Saito, Dynamic heterogeneity in the folding/unfolding transitions of FiP35, JOURNAL OF CHEMICAL PHYSICS, 10.1063/1.4916641, 142, 13, 135101, 2015.04, Molecular dynamics simulations have become an important tool in studying protein dynamics over the last few decades. Atomistic simulations on the order of micro-to milliseconds are becoming feasible and are used to study the state-of-the-art experiments in atomistic detail. Yet, analyzing the high-dimensional-long-temporal trajectory data is still a challenging task and sometimes leads to contradictory results depending on the analyses. To reveal the dynamic aspect of the trajectory, here we propose a simple approach which uses a time correlation function matrix and apply to the folding/unfolding trajectory of FiP35 WW domain [Shaw et al., Science 330, 341 (2010)]. The approach successfully characterizes the slowest mode corresponding to the folding/unfolding transitions and determines the free energy barrier indicating that FiP35 is not an incipient downhill folder. The transition dynamics analysis further reveals that the folding/unfolding transition is highly heterogeneous, e.g., the transition path time varies by similar to 100 fold. We identify two misfolded states and show that the dynamic heterogeneity in the folding/unfolding transitions originates from the trajectory being trapped in the misfolded and half-folded intermediate states rather than the diffusion driven by a thermal noise. The current results help reconcile the conflicting interpretations of the folding mechanism and highlight the complexity in the folding dynamics. This further motivates the need to understand the transition dynamics beyond a simple free energy picture using simulations and single-molecule experiments. (c) 2015 AIP Publishing LLC.. |
| 21. |
Puja Goyal, Hu-Jun Qian, Stephan Irle, Xiya Lu, Daniel Roston, Toshifumi Mori, Marcus Elstner, Qiang Cui, Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models, JOURNAL OF PHYSICAL CHEMISTRY B, 10.1021/jp503372v, 118, 38, 11007-11027, 2014.09, We discuss the description of water and hydration effects that employs an approximate density functional theory, DFTB3, in either a full QM or QM/MM framework. The goal is to explore, with the current formulation of DFTB3, the performance of this method for treating water in different chemical environments, the magnitude and nature of changes required to improve its performance, and factors that dictate its applicability to reactions in the condensed phase in a QM/MM framework. A relatively minor change (on the scale of k(B)T) in the O-H repulsive potential is observed to substantially improve the structural properties of bulk water under ambient conditions; modest improvements are also seen in dynamic properties of bulk water. This simple change also improves the description of protonated water clusters, a solvated proton, and to a more limited degree, a solvated hydroxide. By comparing results from DFTB3 models that differ in the description of water, we confirm that proton transfer energetics are adequately described by the standard DFTB3/3OB model for meaningful mechanistic analyses. For QM/MM applications, a robust parametrization of QM-MM interactions requires an explicit consideration of condensed phase properties, for which an efficient sampling technique was developed recently and is reviewed here. The discussions help make clear the value and limitations of DFTB3 based simulations, as well as the developments needed to further improve the accuracy and transferability of the methodology.. |
| 22. |
Toshifumi Mori, Robert J. Hamers, Joel A. Pedersen, Qiang Cui, Integrated Hamiltonian Sampling: A Simple and Versatile Method for Free Energy Simulations and Conformational Sampling, JOURNAL OF PHYSICAL CHEMISTRY B, 10.1021/jp501339t, 118, 28, 8210-8220, 2014.07, Motivated by specific applications and the recent work of Gao and co-workers on integrated tempering sampling (ITS), we have developed a novel sampling approach referred to as integrated Hamiltonian sampling (IHS). IHS is straightforward to implement and complementary to existing methods for free energy simulation and enhanced configurational sampling. The method carries out sampling using an effective Hamiltonian constructed by integrating the Boltzmann distributions of a series of Hamiltonians. By judiciously selecting the weights of the different Hamiltonians, one achieves rapid transitions among the energy landscapes that underlie different Hamiltonians and therefore an efficient sampling of important regions of the conformational space. Along this line, IHS shares similar motivations as the enveloping distribution sampling (EDS) approach of van Gunsteren and co-workers, although the ways that distributions of different Hamiltonians are integrated are rather different in IHS and EDS. Specifically, we report efficient ways for determining the weights using a combination of histogram flattening and weighted histogram analysis approaches, which make it straightforward to include many end-state and intermediate Hamiltonians in IHS so as to enhance its flexibility. Using several relatively simple condensed phase examples, we illustrate the implementation and application of IHS as well as potential developments for the near future. The relation of IHS to several related sampling methods such as Hamiltonian replica exchange molecular dynamics and A-dynamics is also briefly discussed.. |
| 23. |
Baptiste Joalland, Toshifumi Mori, Todd J. Martinez, Arthur G. Suits, Photochemical Dynamics of Ethylene Cation C2H4+, JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 10.1021/jz500352x, 5, 8, 1467-1471, 2014.04, We present a theoretical study of the nonadiabatic effects in ethylene cation C2H4+, the simplest pi radical cation, after photoexcitation to its three lowest doublet excited states. Two families of conical intersections are found, with minimum energy structures characterized by planar and twisted geometries. Ab initio multiple spawning dynamical calculations suggest that the competition between these relaxation pathways depends strongly on the initial excited state, with excited state lifetimes in the 30-60 fs range. Ultrafast decay via planar geometries deposits the molecule near a bridged minimum on the ground state, allowing prompt H migration events. The alternative pathway mediated by torsional motion induces important backspawned population transfer promoted by hindered rotations. The results allow us to revisit earlier vibrationally-mediated photodissociation experiments and shed light on the electronic relaxation dynamics of a prototypical radical cation subject to strong vibronic interactions.. |
| 24. |
Toshifumi Mori, Robert J. Hamers, Joel A. Pedersen, Qiang Cui, An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic Surfaces, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10.1021/ct400487e, 9, 11, 5059-5069, 2013.11, Identifying factors that control the strength and specificity of interactions between peptides and nanoparticles is essential for understanding the potential beneficial and deleterious effects of nanoparticles on biological systems. Computer simulations are valuable in this context, although the reliability of such calculations depends on the force field and sampling algorithm, as well as how the binding constant and binding free energy are defined; the latter must be carefully defined with a clear connection to microscopic models based on statistical mechanics. Using the example of formate binding to the rutile titanium dioxide (TiO2) (110) surface, we demonstrate that a reliable description of the binding process requires an explicit consideration of changes in the solvation state of the binding site. Specifically, we carry out metadynamics simulations in which the solvent coordination number of the binding site, s, is introduced as a collective variable in addition to the vertical distance of the adsorbate to the surface (z). The resulting two-dimensional potential of mean force (2D-PMF) clearly shows that explicitly including the local desolvation of the binding site on the TiO2 surface strongly impacts the convergence and result of the binding free energy calculations. Projecting the 2D-PMF into a one-dimensional PMF along either z or s leads to large errors in the free energy barriers. Results from metadynamics simulations are quantitatively supported by independent alchemical free energy simulations, in which the solvation state of the binding site is also carefully considered by explicitly introducing water molecules to the binding site as the adsorbate is decoupled from the system. On the other hand, preliminary committor analysis for the approximate transition state ensemble constructed based on the 2D-PMF suggests that to properly describe the binding/unbinding kinetics, variables beyond s and z, such as those describing the hydrogen bonding pattern of the adsorbate and surface water, need to be included. We expect that the insights and computational methodologies established in this work will be generally applicable to the analysis of binding interactions between highly charged adsorbates and ionic surfaces in solution, such as those implicated in peptide/nanoparticle binding and biomineralization processes.. |
| 25. |
Mori T, Martínez TJ, Exploring the Conical Intersection Seam: The Seam Space Nudged Elastic Band Method., Journal of chemical theory and computation, 10.1021/ct300892t, 9, 2, 1155-1163, 2013.02. |
| 26. |
Thomas S. Kuhlman, William J. Glover, Toshifumi Mori, Klaus B. Moller, Todd J. Martinez, Between ethylene and polyenes - the non-adiabatic dynamics of cis-dienes, FARADAY DISCUSSIONS, 10.1039/c2fd20055d, 157, 193-212, 2012.04, Using Ab Initio Multiple Spawning (AIMS) with a Multi-State Multi-Reference Perturbation theory (MS-MR-CASPT2) treatment of the electronic structure, we have simulated the non-adiabatic excited state dynamics of cyclopentadiene (CPD) and 1,2,3,4-tetramethyl-cyclopentadiene (Me-4-CPD) following excitation to S-1. It is observed that torsion around the carbon-carbon double bonds is essential in reaching a conical intersection seam connecting S-1 and S-0. We identify two timescales; the induction time from excitation to the onset of population transfer back to S-0 (CPD: similar to 25 fs, Me-4-CPD: similar to 71 fs) and the half-life of the subsequent population transfer (CPD: similar to 28 fs, Me-4-CPD: similar to 48 fs). The longer timescales for Me4-CPD are a kinematic consequence of the inertia of the substituents impeding the essential out-of-plane motion that leads to the conical intersection seam. A bifurcation is observed on S1 leading to population transfer being attributable, in a 5 : 2 ratio for CPD and 7 : 2 ratio for Me-4-CPD, to two closely related conical intersections. Calculated time-resolved photoelectron spectra are in excellent agreement with experimental spectra validating the simulation results.. |
| 27. |
Toshifumi Mori, William J. Glover, Michael S. Schuurman, Todd J. Martinez, Role of Rydberg States in the Photochemical Dynamics of Ethylene, JOURNAL OF PHYSICAL CHEMISTRY A, 10.1021/jp2097185, 116, 11, 2808-2818, 2012.03, We use the ab initio multiple spawning method with potential energy surfaces and nonadiabatic coupling vectors computed from multistate multireference perturbation theory (MSPT2) to follow the dynamics of ethylene after photoexcitation. We introduce an analytic formulation for the nonadiabatic coupling vector in the context of MSPT2 calculations. We explicitly include the low-lying 3s Rydberg state which has been neglected in previous ab initio molecular dynamics studies of this process. We find that although the 3s Rydberg state lies below the optically bright pi pi* state, little population gets trapped on this state. Instead, the 3s Rydberg state is largely a spectator in the photodynamics, with little effect on the quenching mechanism or excited state lifetime. We predict the time-resolved photoelectron spectrum for ethylene and point out the signature of Rydberg state involvement that should be easily observed.. |
| 28. |
Toshifumi Mori, Katsuhiro Nakano, Shigeki Kato, Conical intersections of free energy surfaces in solution: Effect of electron correlation on a protonated Schiff base in methanol solution, JOURNAL OF CHEMICAL PHYSICS, 10.1063/1.3472033, 133, 6, 064107, 2010.08, The minimum energy conical intersection (MECI) optimization method with taking account of the dynamic electron correlation effect [T. Mori and S. Kato, Chem. Phys. Lett. 476, 97 (2009)] is extended to locate the MECI of nonequilibrium free energy surfaces in solution. A multistate electronic perturbation theory is introduced into the nonequilibrium free energy formula, which is defined as a function of solute and solvation coordinates. The analytical free energy gradient and interstate coupling vectors are derived, and are applied to locate MECIs in solution. The present method is applied to study the cis-trans photoisomerization reaction of a protonated Schiff base molecule (PSB3) in methanol (MeOH) solution. It is found that the effect of dynamic electron correlation largely lowers the energy of S(1) state. We also show that the solvation effect strongly stabilizes the MECI obtained by twisting the terminal C=N bond to become accessible in MeOH solution, whereas the conical intersection is found to be unstable in gas phase. The present study indicates that both electron correlation and solvation effects are important in the photoisomerization reaction of PSB3. The effect of counterion is also examined, and seems to be rather small in solution. The structures of free energy surfaces around MECIs are also discussed. (C) 2010 American Institute of Physics. [doi:10.1063/1.3472033]. |
| 29. |
Toshifumi Mori, Shigeki Kato, Dynamic electron correlation effect on conical intersections in photochemical ring-opening reaction of cyclohexadiene: MS-CASPT2 study, CHEMICAL PHYSICS LETTERS, 10.1016/j.cplett.2009.05.067, 476, 1-3, 97-100, 2009.07, A method to locate minimum energy conical intersection (MECI) points with the analytical derivative technique for multistate complete active space second-order perturbation theory is presented. The photochemical ring-opening reaction of cyclohexadiene (CHD) is revisited to examine the effect of dynamic electron correlation on MECI properties. The geometries as well as potential energy landscapes of CHD are found to change remarkably. The energy difference gradient (g) and interstate coupling (h) vectors consisting the branching plane of MECI are also strongly affected. These results indicate the importance of accurate potential energy surfaces for fully understanding photochemical reactions. (C) 2009 Elsevier B.V. All rights reserved.. |
| 30. |
Toshifumi Mori, Shigeki Kato, Grignard Reagents in Solution: Theoretical Study of the Equilibria and the Reaction with a Carbonyl Compound in Diethyl Ether Solvent, JOURNAL OF PHYSICAL CHEMISTRY A, 10.1021/jp9009788, 113, 21, 6158-6165, 2009.05, The equilibria of Grignard reagents, CH(3)MgCl and CH(3)MgBr, in diethyl ether (Et(2)O) solvent as well as the reaction of the reagents with acetone are studied theoretically. To describe the equilibria and reactions in Et(2)O solvent, we employ the reference interaction site model self-consistent field method with the second-order Moller-Plesset perturbation (RISM-MP2) free energy gradient method. Since the solvent molecules strongly coordinate to the Grignard reagents, we construct a cluster model by including several Et(2)O molecules into the quantum mechanical region and embed it into the bulk solvent. We propose that, instead of the traditionally accepted cyclic dimer, the linear form of dimer is as stable as the monomer pair and participates in the equilibria. For the reaction with acetone, two important reaction paths (i.e., monomeric and linear dimeric paths) are studied. It is found that the barrier height for the monomeric path is much higher than that for the linear dimeric path, indicating that the reaction of the Grignard reagent with acetone proceeds through the linear dimeric reaction path. The change of solvation structure during the reaction is examined. On the basis of the calculated free energy profiles, the entire reaction mechanisms of the Grignard reagents with aliphatic ketones in Et(2)O solvent are discussed.. |
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Toshifumi Mori, Shigeki Kato, Analytical RISM-MP2 free energy gradient method: Application to the Schlenk equilibrium of Grignard reagent, CHEMICAL PHYSICS LETTERS, 10.1016/j.cplett.2007.02.018, 437, 1-3, 159-163, 2007.03, We present a method to evaluate the analytical gradient of reference interaction site model Moller-Plesset second order free energy with respect to solute nuclear coordinates. It is applied to calculate the geometries and energies in the equilibria of the Grignard reagent (CH3MgCl) in dimethylether solvent. The Mg-Mg and Mg-Cl distances as well as the binding energies of solvents are largely affected by the dynamical electron correlation. The solvent effect on the Schlenk equilibrium is examined. (c) 2007 Elsevier B.V. All rights reserved.. |
