Complex molecular systems: a frontier of molecular science
This themed issue includes a collection of articles on complex molecular systems: supramolecules, biomolecules and interfaces.
Harnessing complexity in molecular self-assembly using computer simulations
Computer simulations offer a powerful strategy to explore self-assembly with atomic resolution. Here, we review recent computational studies focusing on both thermodynamic and kinetic aspects.
Multiscale methods framework: self-consistent coupling of molecular theory of solvation with quantum chemistry, molecular simulations, and dissipative particle dynamics
In this work, we will address different aspects of self-consistent field coupling of computational chemistry methods at different time and length scales in modern materials and biomolecular science.
Two dimensional crowding effects on protein folding at interfaces observed by chiral vibrational sum frequency generation spectroscopy
Vibrational sum frequency generation studies demonstrate the effects of two-dimensional molecular crowding on protein folding at interfaces.
Structure of in cell protein crystals containing organometallic complexes
The molecular structures of in cell protein crystals containing organometallic Pd(allyl) complexes were determined by performing microfocus X-ray diffraction experiments.
The first successful observation of in-cell NMR signals of DNA and RNA in living human cells
The first observation of NMR signals of DNA/RNA introduced into living human cells by means of pore formation by SLO and resealing.
The effect of regioisomerism on the photophysical properties of alkylated-naphthalene liquids
Novel alkylated naphthalene liquids with a correlation among the 1- and 2-regioisomeric chemical structures and their photophysical, calorimetric and rheological properties are presented.
The C-terminal cytidine deaminase domain of APOBEC3G itself undergoes intersegmental transfer for a target search, as revealed by real-time NMR monitoring
The deamination activity of A3G-CTD was first increased, but then decreased, which indicated that A3G undergoes the intersegmental transfer.
Contiguous multiple π-coordination of π-conjugated polyenes: bonding nature and charge delocalization behaviour of polyene–(palladium chain) sandwich clusters
We report the bonding nature and charge delocalization behaviour of a series of polyene–(palladium chain) sandwich clusters through systematic 13C NMR analysis and molecular orbital analysis.
Non-invasive force measurement reveals the number of active kinesins on a synaptic vesicle precursor in axonal transport regulated by ARL-8
The regulatory role of ARL-8 in the number of motors carrying a cargo is revealed by non-invasive force measurement.
On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins
The anchoring properties of an asparagine (Asn) residue to its local backbone environment in turn model peptides is characterized using gas phase laser spectroscopy and compared to crystallized protein structures.
Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation
Temperature REMD reveals how local chemical changes can result in markedly differing conformational landscapes for DNA and RNA hairpin loops.
The aggregation of an alkyl–C60 derivative as a function of concentration, temperature and solvent type
Contrast-variation SANS, SAXS, NMR and ITC measurements show that molecule 1 associates into micelles with tunable size based on the solution parameters.
“In situ” observation of the role of chloride ion binding to monkey green sensitive visual pigment by ATR-FTIR spectroscopy
ATR-FTIR spectroscopic study elucidates the novel role of Cl−-binding in primate long-wavelength-sensitive (LWS) visual pigment.
Selective resonance Raman enhancement of large amplitude inter-ring vibrations of (1,2,4,5)cyclophane radical cation; a model of π-stacked dimer radical ions
Delocalized electron resonance selectively enhances Raman scatterings of large amplitude inter-ring vibrations of a π-stacked dimer-form radical cation.
Structural changes of water molecules during photoelectrochemical water oxidation on TiO2 thin film electrodes
Hydrogen bonding networks at the water/TiO2 interface were heavily disrupted and an isolated OH band appeared during photoelectrochemical water oxidation.
Tertiary dynamics of human adult hemoglobin fixed in R and T quaternary structures
We elucidated the coupling between tertiary and quaternary structural dynamics in human adult hemoglobin using time-resolved resonance Raman spectroscopy.
Analysis of the conformational properties of amine ligands at the gold/water interface with QM, MM and QM/MM simulations
We describe a strategy of integrating quantum mechanical (QM), hybrid quantum mechanical/molecular mechanical (QM/MM) and MM simulations to analyze the physical properties of a solid/water interface.
Computational study on the luminescence quantum yields of terbium complexes with 2,2′-bipyridine derivative ligands
The luminescence quantum yields of terbium complexes can be enhanced by replacing moieties whose bending motions induce the rapid quenching processes.
Structure and dynamics of solvent molecules inside the polytheonamide B channel in different environments: a molecular dynamics study
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.
Excited state energy fluctuations in the Fenna–Matthews–Olson complex from molecular dynamics simulations with interpolated chromophore potentials
Environmental fluctuation of pigment excitation energies in the Fenna–Matthews–Olson complex is investigated by our realistic interpolated potential model.
Vibrational relaxation dynamics of β-carotene and its derivatives with substituents on terminal rings in electronically excited states as studied by femtosecond time-resolved stimulated Raman spectroscopy in the near-IR region
Time-resolved near-IR stimulated Raman spectroscopy indicates acceleration of vibrational relaxation in carotenoids by carbonyl substitution on their peripheral rings.
Synthesis and properties of helicene and helicene-like compounds with a cyclopenta[1,2-b:4,3-b′]dithiophene or dithieno[2,3-b:3′,2′-d]heterole skeleton
A series of helicene and helicene-like compounds composed of a cyclopenta[1,2-b:4,3-b′]dithiophene or dithieno[2,3-b:3′,2′-d]heterole moiety and two naphthalene moieties were successfully synthesized from a common synthetic intermediate, 1,1′-binaphtho[2,1-b]thiophene.
Fundamental peak disappears upon binding of a noble gas: a case of the vibrational spectrum of PtCO in an argon matrix
Anharmonic vibrational state calculations were performed for PtCO and Ar–PtCO via the direct vibrational configuration interaction (VCI) method to get insights into the anomalous effect of a solid argon matrix on the vibrational spectra of PtCO.
Visualizing rotational wave functions of electronically excited nitric oxide molecules by using an ion imaging technique
Rotational eigenstates in electronically excited NO molecules have been visualized by a photoion spatial-slice imaging technique.
Two-dimensional structural ordering in a chromophoric ionic liquid for triplet energy migration-based photon upconversion
Triplet exciton diffusion in a chromophoric ionic liquid with two-dimensional order is studied and utilized for photon upconversion.
Microsecond resolved single-molecule FRET time series measurements based on the line confocal optical system combined with hybrid photodetectors
Line confocal microscopy combined with hybrid photodetectors achieves a time resolution of 10 μs and an observation time of approximately 5 ms in single-molecule FRET time series measurements.
Experimental and theoretical investigation of fluorescence solvatochromism of dialkoxyphenyl-pyrene molecules
The uncommon fluorescence solvatochromic behaviour of dialkoxyphenyl-pyrene isomers was confirmed by experiments and elucidated by quantum chemical calculations.
The critical role of dimer formation in monosaccharides binding to human serum albumin
Monosaccharides are found to bind tightly to human serum albumin when a dimeric structure is formed in the binding pocket.
Oxygen induced enhancement of NIR emission in brookite TiO2 powders: comparison with rutile and anatase TiO2 powders
Brookite TiO2 shows visible and NIR emissions. Exposure to O2 weakened the visible emission but enhanced the NIR emission.
A theoretical study on the size-dependence of ground-state proton transfer in phenol–ammonia clusters
Quantum chemical calculations indicate that the critical size of GSPT is n = 9, supporting the IR spectroscopic analysis.
Real-time observation of the photoionization-induced water rearrangement dynamics in the 5-hydroxyindole–water cluster by time-resolved IR spectroscopy
Climbing the ladder by energy accumulation through IVR takes more than a nanosecond.
Structure at the air/water interface in the presence of phenol: a study using heterodyne-detected vibrational sum frequency generation and molecular dynamics simulation
A simple, neutral organic molecule, phenol, forms a specific hydrogen-bonding structure with water at the air/water interface.
Rate constants, processivity, and productive binding ratio of chitinase A revealed by single-molecule analysis
Single-molecule analysis revealed elementary reaction steps and low productive binding ratio of chitinase A.
Successive energy transfer within multiple photosensitizers assembled in a hexameric hemoprotein scaffold
A hexameric hemoprotein scaffold supports photo-excited energy transfer from fluorescein molecules via zinc porphyrins to a single Texas Red molecule.
Site-specific time-resolved FRET reveals local variations in the unfolding mechanism in an apparently two-state protein unfolding transition
Using multi-site time-resolved FRET, it is shown that equilibrium unfolding of monellin is not only heterogeneous, but that the degree of non-cooperativity differs between the sole α-helix and different parts of the β-sheet.
Molecular details of the unique mechanism of chloride transport by a cyanobacterial rhodopsin
An aspartic acid (D85) becomes deprotonated during chloride transport by this cyanobacterial rhodopsin, which possibly serves as a regulatory mechanism.
Stereochemical effects on dynamics in two-component systems of gelators with perfluoroalkyl and alkyl chains as revealed by vibrational circular dichroism
The VCD method was applied to the gelation processes of chiral two-component gel systems.
Spectroscopic characteristics of Rubricoccus marinus xenorhodopsin (RmXeR) and a putative model for its inward H+ transport mechanism
On the basis of functional and spectroscopic characterization, we propose a model for the inward proton transport in RmXeR, a newly discovered microbial rhodopsin.
Sequential microhydration of cationic 5-hydroxyindole (5HI+): infrared photodissociation spectra of 5HI+–Wn clusters (W = H2O, n ≤ 4)
The hydrogen-bonding properties of the acidic OH and NH groups of the 5-hydroxyindole cation are probed by infrared spectroscopy and DFT calculations of its microhydrated clusters.
Low-temperature FTIR spectroscopy provides evidence for protein-bound water molecules in eubacterial light-driven ion pumps
The present FTIR study showed that eubacterial light-driven H+, Na+ and Cl− pump rhodopsins contain strongly hydrogen-bonded water molecule, the functional determinant of light-driven proton pump. This explains well the asymmetric functional conversions of light-driven ion pumps.
Stepwise microhydration of aromatic amide cations: water solvation networks revealed by the infrared spectra of acetanilide+–(H2O)n clusters (n ≤ 3)
The structure of the microhydration network around a prototypical aromatic amide cation was determined by infrared spectroscopy of cold cluster ions and dispersion-corrected DFT calculations.
Solid state vibrational circular dichroism towards molecular recognition: chiral metal complexes intercalated in a clay mineral
The solid state VCD method revealed chirality effects on the intermolecular interaction between Δ- or Λ-[Ru(phen)3]2+ and R or S-BINOL intercalated in a montmorillonite clay.
Protonation/reduction dynamics at the [4Fe–4S] cluster of the hydrogen-forming cofactor in [FeFe]-hydrogenases
FTIR spectroscopy and DFT calculations were used to identify a protonation at the catalytic cofactor of [FeFe]-hydrogenases.
Solvate and protic ionic liquids from aza-crown ethers: synthesis, thermal properties, and LCST behavior
Solvate and protic ILs containing alkyl aza-crown ethers were synthesized, some of which exhibited an LCST-type behavior in water.
Influence of the DNA sequence/length and pH on deaminase activity, as well as the roles of the amino acid residues around the catalytic center of APOBEC3F
The roles of the amino acid residues responsible for the deaminase activity of APOBEC3F were identified by mutation analysis.
Molecular rotors confined at an ordered 2D interface
Different internal molecular motions of fluorescent rotors were found in a 3D environment and at the 2D interface.
Single-component supported lipid bilayers probed using broadband nonlinear optics
Broadband SFG spectroscopy is shown to offer considerable advantages over scanning systems in terms of signal-to-noise ratios when probing well-formed single-component supported lipid bilayers formed from zwitterionic lipids with PC headgroups.
Effect of ligand binding on a protein with a complex folding landscape
Ligand binding to adenylate kinase stabilizes it against folding much less than expected.
Effects of third-order susceptibility in sum frequency generation spectra: a molecular dynamics study in liquid water
χ (2) and χ(3) at charged interfaces in SFG spectroscopy are distinctively calculated using MD simulations.
Paramagnetic ionic plastic crystals containing the octamethylferrocenium cation: counteranion dependence of phase transitions and crystal structures
Octamethylferrocenium salts with various anions exhibit paramagnetic plastic phases at or above room temperature.
Intermolecular charge fluxes and far-infrared spectral intensities of liquid formamide
Intermolecular charge fluxes induced by hydrogen-bond length modulations occurring upon molecular librations lead to intensity enhancement of the far-infrared spectrum.
About this collection
Complex molecular systems provide new, fundamental problems that give rise to a need for further research. Importantly, the realization of efficient synergy between theory and experiment on complex molecular systems has become possible only recently, thanks to significant developments in technology and methodology in measurements (e.g., lasers, detectors, and optics) and computations (e.g., super computers).
Guest Editors Tahei Tahara (RIKEN), Akio Kitao (University of Tokyo), Yasuhisa Mizutani (Osaka University), Hideki Kandori (Nagoya Institute of Technology) and Masaaki Fujii (Tokyo Institute of Technology), are delighted to introduce this themed issue which brings together the most recent studies of this important and emerging field of physical chemistry and chemical physics.