The 10 most-cited articles in The Journal of Physical Chemistry, 2016

Transient absorption, resonance Raman, and vibrational coherence spectroscopies are used to investigate the mechanisms of NO and O₂ binding to WT Tt H-NOX and its P115A mutant. Vibrational coherence spectra of the oxy complexes provide clear evidence for the enhancement of an iron–histidine mode near 217 cm–¹ following photoexcitation, which indicates that O₂ can be dissociated in these proteins. However, the quantum yield of O₂ photolysis is low, particularly in the wild type (≲3%). Geminate recombination of O₂ and NO in both of these proteins is very fast (∼1.4 × 10¹¹ s–¹) and highly efficient. We show that the distal heme pocket of the H-NOX system forms an efficient trap that limits the O₂ off-rate and determines the overall affinity. The distal pocket hydrogen bond, which appears to be stronger in the P115A mutant, may help retard the O₂ ligand from escaping into the solvent following either photoinduced or thermal dissociation. This, along with a strengthening of the Fe–O₂ bond that is correlated with the significant heme ruffing and saddling distortions, explains the…

Carbon–hydrogen (C–H) vibration modes serve as key probes in the chemical identification of hydrocarbons and in vibrational sum-frequency generation spectroscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a challenge from a theoretical viewpoint. In this work, we present a detailed study of the C–H stretching region of dimethyl sulfoxide using a new ab initio molecular dynamics (AIMD) module that we have implemented in NWChem. Through a combination of AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effects in this system. Comprehensive anharmonic normal mode analysis of the C–H stretching region casts doubt upon previous experimental assignments of the shoulder on the symmetric C–H stretching peak. In addition, our AIMD simulations also show significant broadening of the in-phase symmetric C–H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.

The article presents the results of spectroscopic studies of 4-(5-methyl-1,3,4-thiadiazol-2-yl)benzene-1,3-diol (C1) and 4-(5-heptyl-1,3,4-thiadiazol-2-yl)benzene-1,3-diol (C7) in organic solvent solutions. Depending on the concentration of the compound used, three bands were observed in the fluorescence emission spectra of the compounds in DMSO solutions. A single band was observed in methanol, propan-2-ol, or ethanol. The significantly shortened fluorescence lifetimes and the different shapes of circular dichroism (CD) spectra clearly indicate association of the fluorescence effects with the aggregation processes in the analyzed compounds. The differences in the course of the CD spectra also imply an effect of the substituent group structure on the molecule aggregation interactions. Therefore, it has been postulated that the occurrence of the different spectral forms induced by changes in the compound concentration may be related to the aggregation effects of C1 and C7 molecules, which are also induced by differences in the alkyl substituent structure.

In this work, we utilize classical polymer density functional theory (DFT) to study gelation in systems containing colloidal particles onto which polymers are grafted. The solution conditions are such that the corresponding bulk system displays a lower critical solution temperature (LCST). We specifically compare our predictions with experimental results by Shay et al. (J. Rheol. 2001, 45, 913–927), who investigated temperature response in aqueous dispersions containing polystyrene particles (PS), with grafted 45-mer poly(ethylene oxide) (PEO) chains. Our DFT treatment is based on a model for aqueous PEO solutions that was originally developed by Karlstrom for bulk solutions. In this model, monomers are assumed to be in either of two classes of states, labeled A and B, where B is more solvophobic than A. On the other hand, the degeneracy of B exceeds that of A, causing the population of solvophobic monomers to increase with temperature. In agreement with experimental findings by Shay et al., we locate gelation at temperatures considerably below TΘ, and far below the LCST for such…

We employ molecular dynamics simulations of n-octane near a layered graphene surface to study the related phenomena of solvation, density fluctuations, wettability, and structure and dynamics of n-octane molecules in the inhomogeneous interfacial environment. That solvation in bulk n-octane displays a lengthscale-dependent crossover similar to that of hydrophobic solvation in water is known. Here we show that, near an extended graphene interface having attractive interactions with n-octane, lengthscale-dependent solvation is similar to that in the bulk and displays a small to large crossover. However, as the n-octane–graphene interactions are reduced to make the surface increasingly solvophobic, the crossover behavior is modulated and essentially absent near the most solvophobic surfaces, similar to that in water near hydrophobic interfaces. We show that the macroscopic measure of wettability, namely, the contact angle, characterizes n-octane–graphene coupling over a limited range of attractions. In contrast, molecular measures such as the free energy of cavity formation or the…

The aldol reaction catalyzed by an amine-substituted mesoporous silica nanoparticle (amine-MSN) surface was investigated using a large molecular cluster model (Si₃₉₂O₉₅₈C₆NH₃₆₁) combined with the surface integrated molecular orbital/molecular mechanics (SIMOMM) and fragment molecular orbital (FMO) methods. Three distinct pathways for the carbinolamine formation, the first step of the amine-catalyzed aldol reaction, are proposed and investigated in order to elucidate the role of the silanol environment on the catalytic capability of the amine-MSN material. The computational study reveals that the most likely mechanism involves the silanol groups actively participating in the reaction, forming and breaking covalent bonds in the carbinolamine step. Therefore, the active participation of MSN silanol groups in the reaction mechanism leads to a significant reduction in the overall energy barrier for the carbinolamine formation. In addition, a comparison between the findings using a minimal cluster model and the Si₃₉₂O₉₅₈C₆NH₃₆₁ cluster suggests that the use of larger models is important…

The unique structure of cholesterol and its role in modulating lipid translocation (flip-flop) were examined using sum-frequency vibrational spectroscopy (SFVS). Two structural analogues of cholesterolcholestanol and cholestenewere examined to explore the influence of ring rigidity and amphiphilicity on controlling distearoylphosphocholine (DSPC) flip-flop. Kinetic rates for DSPC flip-flop were determined as a function of sterol concentration and temperature. All three sterols increased the rate of DSPC flip-flop in a concentration-dependent manner following the order cholestene > cholestanol > cholesterol. Rates of DSPC flip-flop were used to calculate the thermodynamic activation free energy barrier (ΔG‡) in the presence of cholesterol, cholestanol, and cholestene. The acyl chain gauche content of DSPC, mean lipid area, and membrane compressibility were correlated to observed trends in ΔG‡. ΔG‡ for DSPC flip-flop showed a strong positive correlation with the molar compression modulus (K*) of the membrane, influenced by the type and concentration of the sterol added.…

The formation of pluronic triblock copolymer (F127)–cholesterol-based niosome and its interaction with sugar (sucrose) molecules have been investigated. The morphology of F127–cholesterol -based niosome in the presence of sucrose has been successfully demonstrated using dynamic light scattering (DLS) and transmission electron microscopic (TEM) techniques. The DLS profiles and TEM images clearly suggest that the size of the niosome aggregates increases significantly in the presence of sucrose. In addition to structural characterization, a detailed comparative fluorescence resonance energy transfer (FRET) study has been carried out in these F127-containing aggregates, involving coumarin 153 (C153) as donor (D) and rhodamine 6G (R6G) as an acceptor (A) to monitor the dynamic heterogeneity of the systems. Besides, time-resolved anisotropy and fluorescence correlation spectroscopy measurements have been carried out to monitor the rotational and lateral diffusion motion in these F127–cholesterol-based aggregates using C153 and R6G, respectively. During the course of FRET study, we have…

The [Ru(II)–NO⁺] group affects the structure and chemical reactivity of nitrosylruthenium(II) complexes. A characteristic infrared absorption band due to the nitrosyl (NO) stretching motion is shown in the frequency region 1800–1900 cm–¹. In this work, linear infrared (IR) and nonlinear IR methods, including pump–probe and two-dimensional (2D) IR, were utilized to study the structures and dynamics of two isomeric nitrosylruthenium complexes [Ru(OAc)(2mqn)₂NO] (H2mqn = 2-methyl-8-quinolinol) in cis and trans isomeric configurations in a weak polar solvent (CDCl₃). Using the NO stretching mode as a vibrational probe, information about local structural dynamics of the Ru complex as well as solvent fluctuation dynamics was obtained. In particular, a “structured” solvent environment is believed to form in the vicinity of the NO group in the case of the cis isomer with the aid of a neighboring OAc ligand, which is the reason for more efficient vibrational relaxation but more inhomogeneously distributed solvent and thus associated slower spectral diffusion. Our results also suggest a more…

For assistance in the design of the next generation of nanomaterials that are functional and have minimal health and safety concerns, it is imperative to establish causality, rather than correlations, in how properties of nanomaterials determine biological and environmental outcomes. Due to the vast design space available and the complexity of nano/bio interfaces, theoretical and computational studies are expected to play a major role in this context. In this minireview, we highlight opportunities and pressing challenges for theoretical and computational chemistry approaches to explore the relevant physicochemical processes that span broad length and time scales. We focus discussions on a bottom-up framework that relies on the determination of correct intermolecular forces, accurate molecular dynamics, and coarse-graining procedures to systematically bridge the scales, although top-down approaches are also effective at providing insights for many problems such as the effects of nanoparticles on biological membranes.