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Themed collection Complex molecular systems: supramolecules, biomolecules and interfaces

51 items
Editorial

Complex molecular systems: a frontier of molecular science

This themed issue includes a collection of articles on complex molecular systems: supramolecules, biomolecules and interfaces.

Graphical abstract: Complex molecular systems: a frontier of molecular science
Perspective

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.

Graphical abstract: Harnessing complexity in molecular self-assembly using computer simulations
Perspective

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.

Graphical abstract: Multiscale methods framework: self-consistent coupling of molecular theory of solvation with quantum chemistry, molecular simulations, and dissipative particle dynamics
Communication

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.

Graphical abstract: Structure of in cell protein crystals containing organometallic complexes
Communication

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.

Graphical abstract: The first successful observation of in-cell NMR signals of DNA and RNA in living human cells
From the themed collection: 2018 PCCP HOT Articles
Communication

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.

Graphical abstract: The effect of regioisomerism on the photophysical properties of alkylated-naphthalene liquids
From the themed collection: 2018 PCCP HOT Articles
Communication

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.

Graphical abstract: The C-terminal cytidine deaminase domain of APOBEC3G itself undergoes intersegmental transfer for a target search, as revealed by real-time NMR monitoring
From the themed collection: 2018 PCCP HOT Articles
Paper

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.

Graphical abstract: Contiguous multiple π-coordination of π-conjugated polyenes: bonding nature and charge delocalization behaviour of polyene–(palladium chain) sandwich clusters
Open Access Paper

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.

Graphical abstract: Non-invasive force measurement reveals the number of active kinesins on a synaptic vesicle precursor in axonal transport regulated by ARL-8
Paper

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.

Graphical abstract: On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins
Open Access Paper

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.

Graphical abstract: Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation
Open Access Paper

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.

Graphical abstract: The aggregation of an alkyl–C60 derivative as a function of concentration, temperature and solvent type
Paper

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.

Graphical abstract: “In situ” observation of the role of chloride ion binding to monkey green sensitive visual pigment by ATR-FTIR spectroscopy
Paper

Selective resonance Raman enhancement of large amplitude inter-ring vibrations of [34](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.

Graphical abstract: Selective resonance Raman enhancement of large amplitude inter-ring vibrations of [34](1,2,4,5)cyclophane radical cation; a model of π-stacked dimer radical ions
Paper

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.

Graphical abstract: Structural changes of water molecules during photoelectrochemical water oxidation on TiO2 thin film electrodes
Paper

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.

Graphical abstract: Tertiary dynamics of human adult hemoglobin fixed in R and T quaternary structures
Paper

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.

Graphical abstract: Analysis of the conformational properties of amine ligands at the gold/water interface with QM, MM and QM/MM simulations
From the themed collection: 2018 PCCP HOT Articles
Paper

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.

Graphical abstract: Computational study on the luminescence quantum yields of terbium complexes with 2,2′-bipyridine derivative ligands
Paper

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.

Graphical abstract: Structure and dynamics of solvent molecules inside the polytheonamide B channel in different environments: a molecular dynamics study
Paper

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.

Graphical abstract: Excited state energy fluctuations in the Fenna–Matthews–Olson complex from molecular dynamics simulations with interpolated chromophore potentials
From the themed collection: 2018 PCCP HOT Articles
Paper

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.

Graphical abstract: 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
Paper

Synthesis and properties of [7]helicene and [7]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 [7]helicene and [7]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.

Graphical abstract: Synthesis and properties of [7]helicene and [7]helicene-like compounds with a cyclopenta[1,2-b:4,3-b′]dithiophene or dithieno[2,3-b:3′,2′-d]heterole skeleton
Paper

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.

Graphical abstract: Fundamental peak disappears upon binding of a noble gas: a case of the vibrational spectrum of PtCO in an argon matrix
From the themed collection: 2018 PCCP HOT Articles
Paper

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.

Graphical abstract: Visualizing rotational wave functions of electronically excited nitric oxide molecules by using an ion imaging technique
Paper

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.

Graphical abstract: Two-dimensional structural ordering in a chromophoric ionic liquid for triplet energy migration-based photon upconversion
Paper

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.

Graphical abstract: Microsecond resolved single-molecule FRET time series measurements based on the line confocal optical system combined with hybrid photodetectors
Paper

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.

Graphical abstract: Experimental and theoretical investigation of fluorescence solvatochromism of dialkoxyphenyl-pyrene molecules
Paper

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.

Graphical abstract: The critical role of dimer formation in monosaccharides binding to human serum albumin
Paper

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.

Graphical abstract: Oxygen induced enhancement of NIR emission in brookite TiO2 powders: comparison with rutile and anatase TiO2 powders
Paper

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.

Graphical abstract: A theoretical study on the size-dependence of ground-state proton transfer in phenol–ammonia clusters
Paper

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.

Graphical abstract: Real-time observation of the photoionization-induced water rearrangement dynamics in the 5-hydroxyindole–water cluster by time-resolved IR spectroscopy
Paper

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.

Graphical abstract: Structure at the air/water interface in the presence of phenol: a study using heterodyne-detected vibrational sum frequency generation and molecular dynamics simulation
Paper

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.

Graphical abstract: Rate constants, processivity, and productive binding ratio of chitinase A revealed by single-molecule analysis
Paper

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.

Graphical abstract: Successive energy transfer within multiple photosensitizers assembled in a hexameric hemoprotein scaffold
Paper

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.

Graphical abstract: Site-specific time-resolved FRET reveals local variations in the unfolding mechanism in an apparently two-state protein unfolding transition
Paper

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.

Graphical abstract: Molecular details of the unique mechanism of chloride transport by a cyanobacterial rhodopsin
Paper

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.

Graphical abstract: Stereochemical effects on dynamics in two-component systems of gelators with perfluoroalkyl and alkyl chains as revealed by vibrational circular dichroism
Paper

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.

Graphical abstract: Spectroscopic characteristics of Rubricoccus marinus xenorhodopsin (RmXeR) and a putative model for its inward H+ transport mechanism
Paper

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.

Graphical abstract: Sequential microhydration of cationic 5-hydroxyindole (5HI+): infrared photodissociation spectra of 5HI+–Wn clusters (W = H2O, n ≤ 4)
Paper

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.

Graphical abstract: Low-temperature FTIR spectroscopy provides evidence for protein-bound water molecules in eubacterial light-driven ion pumps
Paper

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.

Graphical abstract: Stepwise microhydration of aromatic amide cations: water solvation networks revealed by the infrared spectra of acetanilide+–(H2O)n clusters (n ≤ 3)
Paper

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.

Graphical abstract: Solid state vibrational circular dichroism towards molecular recognition: chiral metal complexes intercalated in a clay mineral
From the themed collection: 2018 PCCP HOT Articles
Open Access Paper

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.

Graphical abstract: Protonation/reduction dynamics at the [4Fe–4S] cluster of the hydrogen-forming cofactor in [FeFe]-hydrogenases
From the themed collection: 2018 PCCP HOT Articles
Paper

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.

Graphical abstract: Solvate and protic ionic liquids from aza-crown ethers: synthesis, thermal properties, and LCST behavior
Paper

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.

Graphical abstract: 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
Paper

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.

Graphical abstract: Molecular rotors confined at an ordered 2D interface
Paper

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.

Graphical abstract: Single-component supported lipid bilayers probed using broadband nonlinear optics
Paper

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.

Graphical abstract: Effect of ligand binding on a protein with a complex folding landscape
Paper

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.

Graphical abstract: Effects of third-order susceptibility in sum frequency generation spectra: a molecular dynamics study in liquid water
From the themed collection: 2018 PCCP HOT Articles
Paper

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.

Graphical abstract: Paramagnetic ionic plastic crystals containing the octamethylferrocenium cation: counteranion dependence of phase transitions and crystal structures
Paper

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.

Graphical abstract: Intermolecular charge fluxes and far-infrared spectral intensities of liquid formamide
51 items

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.

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