A5047852775- Advanced Chemical Physics Studies
- Spectroscopy and Quantum Chemical Studies
- Quantum, superfluid, helium dynamics
- Molecular Spectroscopy and Structure
- Protein Structure and Dynamics
- Spectroscopy and Laser Applications
- Photochemistry and Electron Transfer Studies
- Atmospheric Ozone and Climate
- Lipid Membrane Structure and Behavior
- Mass Spectrometry Techniques and Applications
- Advanced NMR Techniques and Applications
- Photoreceptor and optogenetics research
- Solid-state spectroscopy and crystallography
- Inorganic Fluorides and Related Compounds
- Hemoglobin structure and function
- Enzyme Structure and Function
- Machine Learning in Materials Science
- Photopolymerization techniques and applications
- Polymer Nanocomposite Synthesis and Irradiation
- Fiber-reinforced polymer composites
- Astrophysics and Star Formation Studies
- Atmospheric chemistry and aerosols
- Spectroscopy Techniques in Biomedical and Chemical Research
- Advanced Proteomics Techniques and Applications
- Molecular Junctions and Nanostructures
RIKEN
2014-2025
University of Tsukuba
2024-2025
RIKEN Center for Computational Science
2024-2025
Pioneer (United States)
2023-2024
Pioneer (Japan)
2019-2024
RIKEN Advanced Science Institute
2014-2017
University of Illinois Urbana-Champaign
2012-2017
The University of Tokyo
2002-2013
University of Yamanashi
2010-2013
Takeda (Japan)
2013
Fluorogenic probes for bioimaging have become essential tools life science and medicine, the key to their development is a precise understanding of mechanisms available fluorescence off/on control, such as photoinduced electron transfer (PeT) Förster resonance energy (FRET). Here we establish new molecular design strategy rationally develop activatable fluorescent probes, which exhibit change in response target biomolecules, by controlling twisted intramolecular charge (TICT) process. This...
Biomolecular condensates have so far been studied in terms of their structural, compositional, and functional properties. However, condensate enzymatic activity, a key aspect cellular metabolism, remains unexplored due to the complexity system. In this study, using combination experimental, computational theoretical techniques, we discovered that non-equilibrium activity which originates from catalytic reactions couples with environment through various feedback mechanisms across five orders...
A circularly polarized ultraviolet (UV) laser pulse may excite a unidirectional valence-type electronic ring current in an oriented molecule, within the duration of few femtoseconds (e.g., tau = 3.5 fs). The mechanism is demonstrated by quantum model simulation for |X |1(1)A(1g) --> |E(+) |4 (1)E(u+) population transfer system, Mg-porphyrin. net generated (I 84.5 microA) at least 100 times stronger than any current, which could be induced means permanent magnetic fields, with present technology.
A procedure to determine optimal vibrational coordinates is developed on the basis of an earlier idea Thompson and Truhlar [J. Chem. Phys. 77, 3031 (1982)]10.1063/1.444226. For a given molecule, these are defined as unitary transform normal that minimizes energy self-consistent-field (VSCF) method for ground state. They justified by fact VSCF in becomes exact two limiting cases: harmonic oscillators, where optimized normal, noninteracting anharmonic which localized individual oscillators....
Abstract The spectroscopic features of protonated water species in dilute acid solutions have been long sought after for understanding the microscopic behavior proton with gas-phase clusters H + (H 2 O) n extensively studied as bottom-up model systems. We present a new protocol calculation infrared (IR) spectra complex systems, which combines fragment-based Coupled Cluster method and anharmonic vibrational quasi-degenerate perturbation theory, demonstrate its accuracy towards complete...
The machine learning (ML) method emerges as an efficient and precise surrogate model for high-level electronic structure theory. Its application has been limited to closed chemical systems without considering external potentials from the surrounding environment. To address this limitation incorporate influence of potentials, polarization effects, long-range interactions between a system its environment, first two terms Taylor expansion electrostatic operator have used extra input existing ML...
GENeralized-Ensemble SImulation System (GENESIS) is a molecular dynamics (MD) software developed to simulate the conformational of single biomolecule, as well interactions in large biomolecular assemblies and between multiple biomolecules cellular environments. To achieve latter purpose, earlier versions GENESIS emphasized high performance atomistic MD simulations on massively parallel supercomputers, with or without graphics processing units (GPUs). Here, we implemented multiscale that...
For polyatomic molecules, n-mode coupling representations of the quartic force field (nMR-QFF) are presented, which include terms up to n normal coordinate couplings in a fourth-order polynomial potential energy function. The computational scheme evaluate third-and derivatives by finite differentiations is fully described. code generate nMR-QFF has been implemented into GAMESS program package and interfaced with vibrational self-consistent (VSCF) correlation corrected VSCF (cc-VSCF) methods....
The vibrational self-consistent field (VSCF) and virtual configuration interaction (VCI) methods are directly combined with ab initio electronic structure calculations for evaluations of the potential energy at VSCF quadrature points. Referred to as direct VCI, respectively, these have been applied anharmonic levels H2O H2CO second-order Mo/ller–Plesset MP2/aug-cc-pVTZ MP2/cc-pVTZ computational levels, respectively. purpose present study is develop a methodology state by examining accuracy...
A quasi-degenerate perturbation method with vibrational self-consistent field (VSCF) reference wavefunction is developed. It simultaneously accounts for strong anharmonic mode–mode coupling among a few states (static correlation) by configuration interaction theory and weak vast number of the other (dynamic theory. general formula derived based on van Vleck An algorithm that selects compact set most important VSCF configurations which contribute to static correlation proposed scheme limit...
The potential energy surface (PES) for the malonaldehyde intramolecular hydrogen atom transfer has been generated with full dimensionality by modified Shepard interpolation method at computational level of second-order Møller–Plesset perturbation theory. reference points have set along reaction path H (51 points), in a three-dimensional space determined geometrical features (219 and region cis- trans-enol isomerization paths (428 so resultant PES was terms ab initio data (energies,...
The use of variationally optimized coordinates, which minimize the vibrational self-consistent field (VSCF) ground state energy with respect to orthogonal transformations has recently been shown improve convergence configuration interaction (VCI) towards exact full VCI [K. Yagi, M. Keçeli, and S. Hirata, J. Chem. Phys. 137, 204118 (2012)]. present paper proposes an incorporation coordinates into coupled cluster (VCC), in past outperform approximate calculations where similar restricted...
Understanding molecular mechanisms of enzymatic reactions is vital importance in biochemistry and biophysics. Here, we introduce new functions hybrid quantum mechanical/molecular mechanical (QM/MM) calculations the GENESIS program to compute minimum-energy pathways (MEPs) free-energy profiles reactions. For this purpose, an interface developed utilize a highly parallel electronic structure program, QSimulate-QM (https://qsimulate.com), calling it as shared library from GENESIS. Second,...
We report an accurate and efficient full dimensional semiclassical ab initio method for calculation of energy level splitting due to tunneling in polyatomic system. The is applied 21-dimensional 9-atomic malonaldehyde molecule. splittings obtained are ΔE(H)=21.2 cm−1 hydrogen atom transfer ΔE(D)=3.0 deuterium transfer, which excellent agreement with the experimental values 21.6 and, 2.9 respectively. believe that present analysis gives final solution longstanding problem.
The symmetric-stretching fundamental (ν1) and the bending first overtone (2ν2) of CO2, which are accidentally degenerate with same symmetry, undergo a Fermi resonance give rise to two Raman bands frequency difference 107 cm(-1) an intensity ratio 2.1. Both can be varied by pressure applied CO2 in condensed phases, has been utilized as spectroscopic geobarometer for minerals inclusion. This study calculates dependence dyad combining embedded-fragment second-order Mo̸ller-Plesset perturbation...
A perturbative extension to optimized coordinate vibrational self-consistent field (oc-VSCF) is proposed based on the quasi-degenerate perturbation theory (QDPT). scheme construct degenerate space (P space) developed, which incorporates configurations and alleviates divergence of expansion due localized coordinates in oc-VSCF (e.g., local O-H stretching modes water). An efficient configuration selection also implemented, screens out Hamiltonian matrix element between P (p) complementary Q...
Quantum mechanics/molecular mechanics (QM/MM) calculations are applied for anharmonic vibrational analyses of biomolecules and solvated molecules. The QM/MM method is implemented into a molecular dynamics (MD) program, GENESIS, by interfacing with external electronic structure programs. Following the geometry optimization harmonic normal-mode analysis based on partial Hessian, potential energy surface (PES) generated from energies gradients calculated at grid points. PES used self-consistent...
A practical and accurate semiclassical method for calculating the tunneling splitting of ground state in polyatomic molecules is presented based on a recent version instanton theory [J. Chem. Phys. 115, 6881 (2001)]. The uses ab initio quantum chemical data potential energy surface without any concomitant extrapolation requires only small number points to get convergence even large molecules. This enables one use an advanced level electronic structure achieve high accuracy result. applied...
A fast algorithm of vibrational second-order Moller-Plesset perturbation theory is proposed, enabling a substantial reduction in the number self-consistent-field (VSCF) configurations that need to be summed calculations. Important are identified priori by assuming reference VSCF wave function approximated well harmonic oscillator functions and fifth- higher-order anharmonicities negligible. The proposed scheme has reduced more than 100 times for formaldehyde, ethylene, furazan with an error...
The authors present a first-principles prediction of the energies eight lowest-lying anharmonic vibrational states CO(2), including fundamental symmetric stretching mode and first overtone bending mode, which undergo strong coupling known as Fermi resonance. They employ coupled-cluster singles, doubles, (perturbative) triples [CCSD(T) CCSDT] in conjunction with range Gaussian basis sets (up to cc-pV5Z, aug-cc-pVQZ, aug-cc-pCVTZ) calculate potential energy surfaces (PESs) molecule, errors...
Significance Denitrification, a form of microbial anaerobic respiration where nitrate is sequentially reduced (NO 3 − → NO 2 N O ) environmentally, biologically, and chemically interesting, as well being medically significant. Some pathogenic bacteria, including the major opportunistic pathogen Pseudomonas aeruginosa , can survive in oxygen-limited environments such biofilms lungs cystic fibrosis patients, owing to denitrification. The current proposal complex formation NO-generating nitrite...
Machine learning (ML) methods have emerged as an efficient surrogate for high-level electronic structure theory, offering precision and computational efficiency. However, the vast conformational chemical space remains challenging when constructing a general force field. Training data sets typically cover only limited region of this space, resulting in poor extrapolation performance. Traditional strategies must address problem by training models from scratch using old new sets. In addition,...