Extended timescale 2D IR probes of proteins: p-cyanoselenophenylalanine

Physical Chemistry Chemical Physics
The importance of dynamics to the function of proteins is well appreciated, but the difficulty in their measurement impedes investigation into their precise role(s). 2D IR spectroscopy is a developing approach for the study of dynamics and has motivated efforts to develop spectrally resolved IR probe groups that enable its application for measuring the dynamics at specific sites in a protein. A challenge with this approach is that the timescales accessible are limited by the vibrational lifetimes of the probes. Toward development of better probes for 2D IR spectroscopy of protein dynamics, we report the characterization of p-cyano-seleno-phenylalanine (CNSePhe), a derivative of the well established IR probe p-cyano-phenylalanine (CNPhe), by FT IR, pump-probe, and 2D IR spectroscopy. The incorporation of the heavy Se atom decouples the CN vibration from the rest in the molecule. Although this leads to a reduction of the transition dipole strength, and thus a reduction in signal...  Read more

Embedded Silicene Nanostructures in Partly-Dehydrogenated Polysilane

Physical Chemistry Chemical Physics
Developing freestanding silicene nanostructures with tunable electronic and magnetic properties is of particular importance for their applications in nanoelectronics, but still faces big challenge. On the basis of first-principles calculation, here, we predict that embedded silicene nanoflakes and nanoribbons can be realized by partly dehydrogenating freestanding polysilane (Si6H6) sheet. Born-Oppenheim molecular dynamic simulations indicate that the embedded silicene nanostructures show good thermal stability at 500 K. In particular, the embedded silicene nanostructures exhibit similar electronics properties as those of isolated ones. These findings imply a practical solution to produce embedded silicene nanostructures from partly dehydrogenated freestanding polysilane.Read more

Entropy-driven homochiral self-sorting of a dynamic library

Chemical Communications
A dynamic mixture of stereoisomeric macrocycles derived from glutamic acid displayed a homochiral self-selection when increasing the acetonitrile content of the aqueous mixed medium. The homochiral self-sorting required the anionic form of the side chains and increased at higher temperature, implying an entropic origin. Conformational analysis (NMR and MD simulations) allowed us to explain the observed behaviour. The results show that entropy can play a role in the homochiral self-sorting in adaptive bio-inspired chemical systems.Read more

Effect of the apical ligand in the geometry and magnetic properties of copper(II)/mesoxalate trinuclear units

Dalton Transactions
Three new heterometallic metal-organic frameworks, namely,{(Ph4P)2[MnCu3(Hmesox)3Br(H2O)]∙H2O}n (1), {(Ph4P)2[CoCu3(Hmesox)3Br]}n (2) and {(Ph4P)2[ZnCu3(Hmesox)3Br]∙2.5H2O}n (3) were prepared and their structure and magnetic properties were investigated (H4mesox = mesoxalic acid, Ph4P+= tetraphenylphosphonium). The structure of all the compounds consist of two interpenetrating chirality-opposite...  Read more

Surface Induced Crystallization of Polymeric Nano-particles: Effect of Surface Roughness

Faraday Discussions
.Molecular dynamics simulations are conducted to study crystallization of a polymeric system as a drop in isolated state and on a surface. It is shown that crystallization kinetics for the polymeric system as a particle on a smooth surface is much faster than in isolated form. We show however as the surface becomes rough the crystallization rate of the polymeric particle decreases. The effect of roughness was compared for two cases of a polymer drop partially (Wenzel state) and fully wetting the cavities (fully confined) on a rough surface. In both cases it was observed that crystallization was slower than that on a smooth surface, and crystal growth rate was decreased by increasing the characteristic roughness ratio. The crystallization on rough surfaces was still faster than that of the isolated polymer drop.Read more

Thermal Conductivity of glassy GeTe4 by First-Principles Molecular Dynamics

Physical Chemistry Chemical Physics
A transient thermal regime is achieved in glassy GeTe4 by first-principles molecular dynamics following the recently proposed ``approach-to-equilibrium" methodology.1 The temporal and spatial evolution of the temperature do comply with the time-dependent solution of the heat equation. We demonstrate that the time scales required to create the hot and the cold parts of the system and observe the resulting approach to equilibrium are accessible to first-principles molecular dynamics. Such a strategy provides the thermal conductivity from the characteristic decay time. We rationalize in detail the impact on the thermal conductivity of the initial temperature difference, the equilibration duration, and the main simulation features.Read more

Photophysics of a Copper Phenanthroline Elucidated by Trajectory and Wavepacket-based Quantum Dynamics: A Synergetic Approach.

Physical Chemistry Chemical Physics
On-the-fly excited state molecular dynamics is an attractive method for studying non-equilibrium processes in excited states and is beginning to emerge as a mature approach much like its ground state counterparts. In contrast to quantum wavepacket dynamics methods, it negates the need for modelling potential energy surfaces, which usually confine nuclear motion within a reduced number of vibrational modes. In addition, on-the-fly molecular dynamics techniques are easily combined with the atomistic description of the solvents (through the QM/MM approach) allowing to explicitly address the effect of the environment. Herein, we study the nonadiabatic relaxation of photoexcited [Cu(dmp)2]+ (dmp = 2,9-dimethyl-1,10-phenanthroline) using QM/MM Trajectory Surface Hopping (TSH). We show that the decay of the initially excited singlet state into the lowest singlet (S1) state occurs within 100 fs, in agreement with previous experiments, and is slightly influenced by the nature of the solvent....  Read more

Insights into the Molecular Interaction between Two Polyoxygenated Cinnamoylcoumarin Derivatives and Human Serum Albumin

Physical Chemistry Chemical Physics
Ligand binding studies on human serum albumin (HSA) are crucial in pharmacological properties determination of drug candidates. Here, two representatives of coumarin–chalcone hybrids were selected and their binding mechanism was identified via thermodynamics techniques, curve resolution analysis and computational methods at molecular levels. The binding parameters were derived using spectroscopic approaches and the results point to only one pocket located near Trp214 residue in subdomain IIA of HSA. The protein tertiary structure was altered during the ligand binding and formed an intermediate structure to create stronger ligand binding interactions. The best binding mode of ligand was initially estimated by docking on an ensemble of HSA crystallographic structures and by molecular dynamics (MD) simulations. Per residue interaction energies were calculated over the MD trajectories as well. Reasonable agreement was found between experimental and theoretical results about the nature...  Read more

Dissociative and non dissociative adsorption of O2 on Cu(111) and CuML/Ru(0001) surfaces: adiabaticy takes over

Physical Chemistry Chemical Physics
The role of spin non-adiabatic effects in the reactivity of O2 on metal surfaces has been a matter of debate for several years. By means of density functional theory with a semi-local exchange-correlation functional, and classical dynamics calculations, we show that the recently observed activated character of O2 adsorption on Cu(111) and CuML/Ru(0001), as well as the delicate interplay between dissociative and non-dissociative O2 sticking on Cu(111) at different surface temperatures, can be explained by assuming an adiabatic evolution of the molecular spin. This suggests that spin adiabaticity during O2 adsorption on metal surfaces could be a more general scenario than anticipated.Read more

The origin of the measured chemical shift of 129Xe in UiO-66 and UiO-67 revealed by DFT investigations

Physical Chemistry Chemical Physics
The NMR chemical shift of the xenon isotope 129Xe inside the metal-organic frameworks (MOFs) UiO-66 and UiO-67 (UiO - University of Oslo) has been investigated both with density functional theory (DFT) and in situ high-pressure 129Xe NMR measurements. The experiments reveal a decrease of the total chemical shift comparing the larger isoreticular MOF (UiO-67) with the smaller one (UiO-66), even though one may expect an increase due to the higher amount of adsorbed Xe atoms. We are able to calculate contributions to the chemical shift individually. This allows us to evaluate the shift inside the different pores independently. To compare the theoretical results with the experimental ones, we performed molecular dynamics simulations of Xe in the MOFs. For this purpose, the pores were completely filled with Xe to gain insight into the distribution of Xe at high pressures. The resulting trend of the total shift agrees well between...  Read more

Effects of the locality of a potential derived from hybrid density functionals on Kohn-Sham orbitals and excited states

Physical Chemistry Chemical Physics
Density functional theory (DFT) has been an essential tool for electronic structure calculations in various fields. In particular, its hybrid method including the Hartree-Fock exchange term remarkably improves the reliability of DFT for chemical applications and computational material design. There are two different types of exchange-correlation potential that can be derived from hybrid functionals. The conventional approach adopts a non-multiplicative potential including the non-local HF exchange operator. Herein, we propose to use a local multiplicative potential as an alternative for accurate excited state calculations. We show that such a local potential can be derived from existing global hybrid functionals using the optimized effective potential method. As a proof-of-concept, we chose PBE0 and investigated its performance for the Caricato benchmark set. Unlike the conventional one, the local potential produced orbital energy gaps with no strong dependence on the mixing ratio as...  Read more

Understanding how cAMP-Dependent Protein Kinase Can Catalyze Phosphoryl Transfer in the Presence of Ca2+ and Sr2+: A QM/MM Study

Physical Chemistry Chemical Physics
Recent experimental results have challenged conventional views on the role metals play in the chemistry of protein kinases because it has been shown that (cAMP)-dependent protein kinase (PKA) is active in the presence of other divalent alkaline earth metal cations besides physiological Mg2+ ions. This has raised the important possibility that Ca2+ may also be a physiological cofactor of protein kinases. In this work, QM/MM calculations, at the DFT and MP2 levels for the QM part, on complete solvated models of PKAc-M2ATP-Substrate ternary complexes, with PKAc as the catalytic subunit of PKA, M standing for Ca2+ or Sr2+ and Substrate standing for SP20 or Kemptide, have been carried out for the overall phosphoryl transfer reaction. In accordance with experimental data, our theoretical results show for the first time at the molecular level how the overall PKAc-catalyzed phosphorylation of SP20, via a dissociative mechanism, is plausible with Ca2+ and Sr2+. The viability of the catalytic...  Read more

Effect of Sb-surfactant on GaInP CuPB type ordering: assessment through dark field TEM and aberration corrected - HAADF

Physical Chemistry Chemical Physics
We report on the effect of Sb on the microstructure of GaInP layers grown by metal organic vapor phase epitaxy (MOVPE). These layers exhibit the CuPtB single variant ordering due to the intentional misorientation of the substrate (Ge(001) substrates with 6º misorientation towards the nearest [111]). The use of Sb as surfactant during the GaInP growth does not modify the type of ordering, but it is found that order parameter (η) decreases with increasing Sb flux. Dark field microscopy reveals a variation of the angle of the antiphase boundaries (APB) with Sb amount. The microstructure is assessed through high angle annular dark field (HAADF) experiments and image simulation revealing Z-contrast loss in APB boundaries due to the superposition of ordered domains.Read more

A multi-fluid model for microstructure formation in polymer membranes

Soft Matter
We develop a multi-fluid model for a ternary polymer solution using the Rayleighian formalism of Doi and Onuki (J. Phys. France 2, 1631, 1992), and give an efficient pseudo-spectral method for solving both the diffusion and momentum equations that result. Subsequently, we find that the numerical simulation is capable of describing systems at the micron length-scale and easily reaches millisecond time-scales. In addition, we characterize the model thermodynamics and kinetics including the (i) phase behavior, (ii) structure of the interfaces, (iii) mutual diffusion coefficients, (iv) bulk spinodal decomposition kinetics with and without hydrodynamics and (v) spinodal decomposition in the presence of an interface with a non-solvent bath. We obtain good qualitative agreement with the expected thermodynamic and kinetic behavior. We also show that a linear stability analysis of the diffusion equation quantitatively predicts the fastest growing mode obtained from simulation and gives insight...  Read more

A structurally characterised redox pair involving an indigo radical: Indigo based redox activity in complexes with one or two [Ru(bpy)2] fragments

Dalton Transactions
The reaction between indigo, H2Ind and {Ru(bpy)2(EtOH)2}2+ in EtOH/NaOH produced the compounds [Ru(bpy)2(HInd)](ClO4) [1]ClO4, rac-{[Ru(bpy)2]2(-Ind)}(ClO4)2 [2](ClO4)2, and meso-{[Ru(bpy)2]2(-Ind)}(ClO4)3 [2](ClO4)3, which were structurally characterised, the latter as the first stable, isolable radical complex of indigo. The redox pair 22+/23+ showed little structural difference as confirmed by DFT calculations. Redox series 1n and 2n were investigated by voltammetry and spectroelectrochemistry (EPR, UV-vis-NIR). Remarkably, the EPR results for 1, 12+, 2+ and 23+ revealed mostly ligand based spin in ruthenium(II) complexes of indigo-derived radical ligands HInd•2, HInd•, Ind•3 or Ind•, in agreement with DFT calculated spin densities. The dominance of the frontier orbitals by the metal-stabilised indigo chromophore is also confirmed by the TD-DFT based assignment of near-infrared absorptions as intra-indigo or ligand-to-ligand charge transfer transitions.Read more

A Threonine Turnstile Defines a Dynamic Amphiphilic Binding Motif in the AAA ATPase p97 Allosteric Binding Site

Organic & Biomolecular Chemistry
The turnstile motion of two neighboring threonines sets up a dynamic side chain interplay that can accommodate both polar and apolar ligands in a small molecule allosteric protein binding site. A computational model based on SAR data and both X-ray and cryo-EM structures of the AAA ATPase p97 was used to analyze the effects of paired threonines at the inhibitor site. Specifically, the Thr side chain hydroxyl groups form a hydrogen bonding network that readily accommodates small, highly polar ligand substituents. Conversely, diametric rotation of the χ1 torsion by 150-180o orients the side chain β-methyl groups into the binding cleft, creating a hydrophobic pocket that can accommodate small, apolar substituents. This motif was found to be critical for rationalizing the affinities of a structurally focused set of inhibitors of p97 covering a >2,000-fold variation in potencies, with a preference for either small-highly polar or small-apolar groups. The threonine turnstile motif was...  Read more

Interlayer Resistance of Misoriented MoS2

Physical Chemistry Chemical Physics
Interlayer misorientation in transition metal dichalcogenides alters the interlayer distance, total energy, the electronic bandstructure, and the vibrational modes, but, its effect on the interlayer resistance is not known. This study quantifies the interlayer resistance of misoriented bilayer MoS2 as a function of misorientation angle, and it shows that interlayer misorientation exponen- tially increases the electron resistivity while leaving the hole resistivity almost unchanged. The physics, determined by the orbital compositions at the high symmetry points, indicates that the trends are generic among the popular semiconducting transition metal dichalcogenides (TMDs). The asymmetrical effect of misorientation on the electron and hole transport can be exploited in the design and optimization of vertical transport devices such as a heterostructure bipolar transis- tor, since it could alter the gain by several orders of magnitude. Density functional theory provides the interlayer...  Read more

Light-induced confinement of electrons in stacked distorted graphene layers – (TD-)DFT study

Physical Chemistry Chemical Physics
Recently observed white-light emission from graphene ceramics cannot be explained by black body radiation theory because of relatively low temperature of the sample. Furthermore intensity of the emission stays at the same level even for temperatures as low as 10 K, indicating purely electronic nature of the observed emission. In this work a model of light emission from locally interacting stacked graphene layers after intense continuous wave laser excitation is proposed. After light-induced sp2 to sp3 change of the hybridization sp2-nanodomain surrounded by sp3 carbon atoms could be created and the electrons can be confined. Using DFT and TD-DFT methods following by molecular-like approach we examine the electronic structure and optical properties of graphene (sp2,sp3)-clusters. We show the quantized and well separated energy...  Read more

A theoretical simulation of small-molecules sensing on s-vacancy SnS2 monolayer

Physical Chemistry Chemical Physics
Using first-principle atomistic simulations, we focus on the electronic structures of small gas molecules (CO, H2O, NH3, NO and NO2) adsorbed on the s-vacancy SnS2 monolayer. The results show that H2O, NH3 and CO molecules are physisorbed on s-vacancy SnS2 monolayer, while NO and NO2 molecules are found to be chemisorbed on s-vacancy SnS2 via strong covalent bonds. Moreover, our calculations show that H2O and NH3 act as charge donors, whereas CO, NO and NO2 gas molecules act as acceptors. Different adsorption behaviors of common gas molecules on the s-vacancy SnS2 provide a feasible way to exploit chemically gas sensor and electrical devices. In particular, our results also show that under applied biaxial strains, adsorption energy and charge transfer of gas molecules on s-vacancy SnS2 monolayer dramatically changed, which indicates that external factors on s-vacancy SnS2 monolayer are highly preferred.Read more

Reaction mechanism of sarcosine oxidase elucidated using FMO and QM/MM methods

Physical Chemistry Chemical Physics
Monomeric sarcosine oxidase (MSOX) is a flavoprotein that oxidizes sarcosine to the corresponding imine product and is widely used in clinical diagnostics to test renal function. In the past decade, several experimental studies have been performed to elucidate the underlying mechanism of this oxidation reaction. However, the details of the molecular mechanism remain unknown. In this study, we theoretically examined three possible reaction mechanisms, namely, the single-electron transfer, hydride-transfer, and polar mechanisms, using the fragment molecular orbital (FMO) and mixed quantum mechanics/molecular mechanics (QM/MM) methods. We found that, of the three possible reaction pathways, the hydride-transfer one is the most energetically favorable. Significantly, the hydrogen is not transferred in the hydride state (H-) but in a hydrogen atom state (H.). Further, a single electron is simultaneously transferred from sarcosine to the flavin through their overlapping orbitals. Therefore,...  Read more