Equilibrium Of Molecules Research Articles

Shear-activation of mechanochemical reactions through molecular deformation.

Mechanical stress can directly activate chemical reactions by reducing the reaction energy barrier. A possible mechanism of suchmechanochemical activation is structural deformation of the reactant species. However, the effect of deformation on the reaction energetics is unclear, especially, for shear stress-driven reactions. Here, we investigated shear stress-driven oligomerization reactions of cyclohexene on silica using a combination of reactive molecular dynamics simulations and ball-on-flat tribometer experiments. Both simulations and experiments captured an exponential increase in reaction yield with shear stress. Elemental analysis of ball-on-flat reaction products revealed the presence of oxygen in the polymers, a trend corroborated by the simulations, highlighting the critical role of surface oxygen atoms in oligomerization reactions. Structural analysis of the reacting molecules in simulations indicated the reactants were deformed just before a reaction occurred. Quantitative evidence of shear-induced deformation was established by comparing bond lengths in cyclohexene molecules in equilibrium and prior to reactions. Nudged elastic band calculations showed that the deformation had a small effect on the transition state energy but notably increased the reactant state energy, ultimately leading to a reduction in the energy barrier. Finally, a quantitative relationship was developed between molecular deformation and energy barrier reduction by mechanical stress.

Susceptibility of Cu(I) transport ATPases to sodium dodecyl sulfate. Relevance of the composition of the micellar phase

Sodium dodecyl sulfate (SDS) is a well-known protein denaturing agent. A less known property of this detergent is that it can activate or inactivate some enzymes at sub-denaturing concentrations. In this work we explore the effect of SDS on the ATPase activity of a hyper-thermophilic and a mesophilic Cu(I) ATPases reconstituted in mixed micelles of phospholipids and a non-denaturing detergent. An iterative procedure was used to evaluate the partition of SDS between the aqueous and the micellar phases, allowing to determine the composition of micelles prepared from phospholipid/detergent mixtures. The incubation of enzymes with SDS in the presence of different amounts of phospholipids reveals that higher SDS concentrations are required to obtain the same degree of inactivation when the initial concentration of phospholipids is increased. Remarkably, we found that, if represented as a function of the mole fraction of SDS in the micelle, the degree of inactivation obtained at different amounts of amphiphiles converges to a single inactivation curve. To interpret this result, we propose a simple model involving active and inactive enzyme molecules in equilibrium. This model allowed us to estimate the Gibbs free energy change for the inactivation process and its derivative with respect to the mole fraction of SDS in the micellar phase, the latter being a measure of the susceptibility of the enzyme to SDS. Our results showed that the inactivation free energy changes are similar for both proteins. Conversely, susceptibility to SDS is significantly lower for the hyperthermophilic ATPase, suggesting an inverse relation between thermophilicity and susceptibility to SDS.

Orientational isomerisation of guest molecules in equilibrium in a tubular host crystal formed via halogen and hydrogen bonding

The orientation of the guest molecules in the one-dimensional tube is reversed in a temperature-dependent manner, and the ratio of the two orientational isomers changes continuously and reversibly from 100 : 0 to 0 : 100 in thermodynamic equilibrium.

Removal of formaldehyde and methylene blue from aqueous solution by adsorption on cerium-doped activated carbon: a comparative study

ABSTRACT The present study deals with the adsorption mechanisms of methylene blue (MB) and formaldehyde (FA) in aqueous solution using cerium-doped activated carbon (Ce/AC). Firstly, the cerium-doped carbon material was synthesised and characterised by scanning electron microscopy–energy dispersive spectrometry (SEM-EDS), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FT-IR). The experimental results obtained have shown that MB and FA molecules were adsorbed onto Ce/AC through various mechanisms. The resulting cation from the dissolution of MB was rapidly adsorbed during the first 5 min, and reached equilibrium after 15 min of contact time. Whereas, the rapid phase of methanediol adsorption, a molecule obtained by reaction of FA with water molecules in equilibrium with its anion, took place during the first 40 min and reached equilibrium within 150 min. The MB adsorption data fitted well Langmuir II isotherm model, while the FA adsorption equilibrium was non-linear. The covered surface by the both two molecules increased linearly with their initial concentration. Also, the FA molecules were more adsorbed compared to MB molecules onto Ce/AC. This result was consistent with the pseudo-second order kinetic model, showing the MB maximum chemisorbed elimination of 76% against 92% for FA. These findings clearly demonstrated the high ability of Ce/AC to adsorb dye and volatile molecules from aqueous environment. Therefore, the Ce/AC is promising material that can be used as an environmentally friendly adsorbent for wastewater treatment purpose.

Towards Near-Exact Solutions of Molecular Electronic Structure: Full Coupled-Cluster Reduction with a Second-Order Perturbative Correction.

We introduce a new augmented adaptation of the recently developed full coupled-cluster reduction (FCCR) with a second-order perturbative correction, abbreviated as FCCR(2). FCCR is a selected coupled-cluster expansion aimed at optimally reducing the excitation manifold and commutator expansions for high-rank excitations for obtaining accurate solutions of the electronic Schödinger equation in a size-extensive manner. The present FCCR(2) enables estimating the residual correlation of FCCR by the second-order perturbative correction E(2) from the complementary space of the FCCR projection manifold. The linear relationship between E(2) and the energy of FCCR(2) allows accurate estimates of near-exact energies for a wide variety of molecules with strong electron correlation. The potential of the method is demonstrated using challenging cases, the ground-state electronic energy of the benzene molecule in equilibrium and stretched geometries, and the isomerization energy of the transition metal complex [Cu(NH3)]2O22+.

A study of the Composition of Tellurium Vapor by the Static Method

The static method with the use of a zero-pressure gauge makes it possible to accurately measure the vapor pressure. The data on the temperature dependence of the unsaturated vapor pressure of the substance (in the absence of the condensed phase) in the static experiment allow determining the vapor’s composition. A multicomponent system consisting of molecules containing i number of atoms is considered. Mathematical methods are developed to study the molecular composition of a multicomponent vapor. In combination with the initial equations, a system of n linear equations with n unknowns is obtained. The system of equations is compatible and has a unique solution, since the determinant composed of the coefficients at the unknown partial pressures of the components is different from zero. The composition of tellurium vapor was studied experimentally by the static method. It is shown that tellurium vapor consists mainly of one-, two-, and four-atom molecules in equilibrium (Te2 = 2Te and Te4 = 2Te2). The processing of the experimental data made allows obtaining the equations of the temperature dependence of the constants and reveal the change in the average number of tellurium atoms in the gas phase in a broad range of pressures and temperatures.

Equilibration of molecules between two compartments through a nanochannel in the presence of osmolytes: a molecular dynamics simulation study.

Using molecular dynamics simulations, we study the equilibration of a system consisting of two nanoscale compartments connected by a carbon nanotube through which small mobile molecules can pass. The system is initially in a state where only one compartment is filled with molecules and the other is empty. When the molecules are allowed to move from the filled compartment to the empty one, the system starts equilibrating and finally reaches an equilibrium state where the molecules are distributed between the two compartments. In the absence of osmolytes, the equilibrium distribution of molecules is simply determined by the relative volumes of the compartments, but in the presence of osmolytes, the distribution is dependent on not only the relative compartment volumes but also the osmolyte properties. To systematically study the effect of osmolytes, we investigate how the number of osmolytes and the strength of the interaction between molecules and osmolytes affect the equilibrium state. Interestingly, we find that osmolytes strongly interacting with molecules can drain the initially filled compartment and induce the complete transfer of molecules to the initially empty compartment. We also study the kinetic and thermodynamic aspects of the equilibration processes.

Information equilibria, subsystem entanglement, and dynamics of the overall entropic descriptors of molecular electronic structure

Overall descriptors of the information (determinicity) and entropy (uncertainty) content of complex molecular states are reexamined. These resultant concepts combine the classical (probability) contributions of Fisher and Shannon, and the relevant nonclassical supplements due to the state phase/current. The information-theoretic principles determining equilibria in molecules and their fragments are explored and the nonadditive part of the global entropy is advocated as a descriptor of the classical index of the quantum entanglement of molecular subsystems. Affinities associated with the probability and phase fluxes are identified and the criterion of vanishing overall information-source is shown to identify the system stationary electronic states. The production of resultant density of the gradient-information is expressed in terms of the conjugate affinities (forces, perturbations) and fluxes (currents, responses). The Schrödinger dynamics of probability and phase components of molecular electronic states is used to determine the temporal evolution of the overall gradient information and complex entropy. The global sources of the resultant information/entropy descriptors are shown to be of purely nonclassical origin, thus identically vanishing in real electronic states, e.g., the nondegenerate ground state of a molecule.

Some observations about MOLPRO

In equilibrium, coordinates of atoms in a molecule are expressed with respect to the origin situated at the center–of–mass of the molecule. In the quantum mechanical software MOLPRO, we have found that the center–of–mass of molecule does not coincide with the origin of the coordinate system. Rather it lies in a random manner. The problem becomes more severe when, for example, one wants to know the separation between two interacting particles in the scattering process. There appears need to make amendment in MOLPRO, so that the origin of coordinate system coincides with the center–of–mass of the molecule in equilibrium.

Quantum Information Measures and Their Use in Chemistry

Background: The resultant measures of the information content in molecular electronic states are revisited. In these overall measures the current-related terms complement the probability functionals of classical Information Theory. The nonclassical Shannon entropy reflects the average magnitude of the state phase distribution, while the related current term in the complementary Fisher measure accounts for the average phase-gradient. Method: These generalized Fisher and Shannon descriptors of the information content in complex electronic states are applied to determine the phase-equilibria in molecules. The vertical and horizontal equilibria in molecules, which mark the extrema of the nonclassical and resultant entropy/information descriptors, respectively, are explored. The requirement, that the resultant measures have common solutions of the associated extreme entropy/information principles, calls for the negative sign of the nonclassical gradient measure. Conclusion: These extrema imply the phase-transformation of molecular electronic states. A separation of the density (modulus) and current (phase) factors in many-electron states is effected using the Harriman-Zumbach-Maschke construction of complex antisymmetric states yielding the specified electron density. A combined description of molecular systems, which accounts for the density and current degrees-of-freedom of electronic states is summarized and continuity equations for the state phase and resultant entropy are discussed. Keywords: Continuity equations, current-information, information continuity, molecular equilibria, phase-entropy/information, entropy.

Incident energy dependence of the scattering dynamics of water molecules on silicon and graphite surfaces: the effect on tangential momentum accommodation

The scattering dynamics of water molecules on solid surfaces was investigated using the molecular beam technique. In contrast to the experiments previously reported in the literature, the range of incident energy was chosen to cover the typical kinetic energies of gas molecules in equilibrium at room temperature (35–130 meV). Even in such a narrow energy range, the angular distribution of scattered molecules is heavily affected by the incident energy, exhibiting both a nearly cosine distribution and a lobular distribution, which has a clear peak close to the specular direction. Interestingly, the tangential momentum accommodation coefficients (TMACs) estimated from the scattering experiments show opposite energy dependences on graphite (0001) and silicon (100) surfaces. As the incident energy increases, the TMAC decreases on the graphite surface, whereas it increases on the silicon surface. These trends can be attributed to the relatively large adsorption energy of water molecules on these surfaces and the atomic-scale surface corrugation, although a rigorous understanding requires further analysis by molecular dynamics simulations. Our findings suggest the need for an elaborate slip-flow model that takes account of the incident energy effect to accurately analyze water vapor flow in micro/nanostructures, which is ubiquitous in nature and engineering applications.

Review ofTychomancy- Michael Strevens,Tychomancy: Inferring Probability from Causal Structure. Cambridge, MA: Harvard University Press (2013), 280 pp., $39.95 (cloth).

Another example Strevens discusses in some detail is Maxwell’s 1859 discovery of the Maxwell-Boltzmann law, according to which the velocity of gas molecules in equilibrium has a Gaussian probability distribution in each direction. As Strevens points out, Maxwell’s original derivation of the distribution, from apparently a priori symmetry assumptions, is not only unsatisfactory, but doesn’t even do justice to Maxwell’s own evidence. Maxwell knew the probabilities, but he didn’t know how he knew. Tychomancy is a welcome philosophical contribution to an important topic. Probabilistic judgements are central to our scientific and everyday understanding of the world, but we know little about how these judgements are formed and what makes them reliable. Strevens addresses these questions in a pleasantly accessible but careful style, combining insights from child psychology, the history of science, and the mathematics of probability. So what guides our probabilistic judgements? From examples like dice one might think they are directly based on physical symmetries, following some principle of indierence. But things are not that simple. We know that a die tossing machine is unlikely to produce the usual probabilistic patterns, despite the physical symmetries of the die. We also realize that if a die is rolled without shaking, then some outcomes are at a disadvantage. Moreover, it is not obvious how physical symmetries enter into evolutionary explanations,

Lubrication by physisorbed molecules in equilibrium with vapor at ambient condition: effects of molecular structure and substrate chemistry.

The effects of physisorbed organic vapor molecules on friction and wear were studied for various materials with different surface chemistries (metals, ceramics, glasses, carbons, polymers) and adsorbed species with distinct functional groups (short linear-chain, branched, and fluorinated alcohols with alkyl chain lengths up to five carbons as well as acetone and n-decane). Friction test results of stainless steel under equilibrium vapor adsorption conditions indicated that the longer chain length of the adsorbed alcohols results in lower friction and that n-pentanol gives the lowest friction and wear among the molecules investigated. The adsorption isotherm measurements revealed that the functional groups of the adsorbed molecules appear to play important roles in lubrication. Friction coefficients that ranged from 0.02 to 0.9 for the various materials in dry and humid environments converged to ∼0.15 for the inorganic solid materials tested in n-pentanol. These findings indicate that the molecular lubrication by the physisorbed species dominates the tribological behaviors of the inorganic solid materials, regardless of bulk mechanical properties. Tribotests using polymeric materials did not show the same lubricating effects for n-pentanol vapor. The failure of n-pentanol to lubricate polymeric materials may be due to vapor ingress into the polymer and the absence of an adsorbed surface layer.

Molecular Dynamics Study of Conserved Water Molecules in PrPc and Pathological Point Mutation T188R

The secondary conformational change of cellular prion protein (PrPc) into scrapie prion protein (PrPsc) is critical important for prion disease including bovine spongiform encephalopathy and Creutzfeldt-Jakob disease.This study performed molecular dynamics simulations of both human prion protein (WT-PrPc) and pathogenic mutant prion protein (T188R) and analyze its conserved water molecules in equilibrium state.Although the secondary structure is not dramatically different, increase of Cα- RMSF occurs not only around mutation point but also in a wide range. This increase of intensity may result from the instability caused by point mutation.Next, we calculated mean residence time for each protein atoms to find conserved water molecules. Residence time is defined that the time from when the water molecule get into the sphere whose center is a protein atom to the evacuation of water molecule from the sphere. We found four conserved water molecule sites in WT-PrPc. Conserved water molecules also keep the higher rotational correlation than water molecules in bulk. These results shows that conserved water molecules are not only wrapped but also fixed by hydrogen bond between conserved water molecule and amino acids.On the other hand, every residence time of T188R decrease compared by WT-PrPc and the rotational relaxation is also faster than WT-PrPc although secondary structure is almost not different. These results show that conserved water molecules cannot survive related to the wide range fluctuation caused by point mutation.

Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy. 1. Principle

Fluorescence correlation spectroscopy (FCS) is a unique tool for investigating microsecond molecular dynamics of complex molecules in equilibrium. However, application of FCS in the study of molecular dynamics has been limited, owing to the complexity in the extraction of physically meaningful information. In this work, we develop a new method that combines FCS and time-correlated single photon counting (TCPSC) to extract unambiguous information about equilibrium dynamics of complex molecular systems. In this method, which we name two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS), we analyze the correlation of the fluorescence photon pairs, referring to the fluorescence lifetime. We first obtain the correlations of the photon pairs with respect to the excitation-emission delay times in the form of a two-dimensional (2D) map. Then, the 2D map is converted to the correlations between different species that have distinct fluorescence lifetimes using inverse Laplace transformation. This 2D FLCS is capable of visualizing the equilibration dynamics of complex molecules with microsecond time resolution at the single-molecule level. We performed a kinetic Monte Carlo simulation of a TCPSC-FCS experiment as a proof-of-principle example. The result clearly shows the validity of the proposed method and its high potential in analyzing the photon data of dynamic systems.

The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field.

An important unsolved problem in materials science is prediction of the thermodynamic stability of organic crystals and their solubility from first principles. Solubility can be defined as the saturating concentration of a molecule within a liquid solvent, where the physical picture is of solvated molecules in equilibrium with their solid phase. Despite the importance of solubility in determining the oral bioavailability of pharmaceuticals, prediction tools are currently limited to quantitative structure-property relationships that are fit to experimental solubility measurements. For the first time, we describe a consistent procedure for the prediction of the structure, thermodynamic stability and solubility of organic crystals from molecular dynamics simulations using the polarizable multipole AMOEBA force field. Our approach is based on a thermodynamic cycle that decomposes standard state solubility into the sum of solid-vapor sublimation and vapor-liquid solvation free energies [Formula: see text], which are computed via the orthogonal space random walk (OSRW) sampling strategy. Application to the n-alkylamides series from aeetamide through octanamide was selected due to the dependence of their solubility on both amide hydrogen bonding and the hydrophobic effect, which are each fundamental to protein structure and solubility. On average, the calculated absolute standard state solubility free energies are accurate to within 1.1 kcal/mol. The experimental trend of decreasing solubility as a function of n-alkylamide chain length is recapitulated by the increasing stability of the crystalline state and to a lesser degree by decreasing favorability of solvation (i.e. the hydrophobic effect). Our results suggest that coupling the polarizable AMOEBA force field with an orthogonal space based free energy algorithm, as implemented in the program Force Field X, is a consistent procedure for predicting the structure, thermodynamic stability and solubility of organic crystals.

Chiral Symmetry Breaking in Crystals of Achiral Polymers

Many achiral polymers crystallize into spherulites with gigantic chirality, as is evident from spectacular images of periodic banding observed in a polarized optical microscope, arising from the twisting of the lamellae making up the spherulites. We present a new mechanism of the spontaneous chiral symmetry breaking, by accounting for topological defects in finite crystalline ribbons made of achiral molecules in equilibrium. We show that disclinations stabilize a twisted helicoidal ribbon, with spontaneous selection of its width and chiral period, which are proportional to each other, as a universal law.

Tribochemical Polymerization of Adsorbed n-Pentanol on SiO2 during Rubbing: When Does It Occur and Is It Responsible for Effective Vapor Phase Lubrication?

The origin and role of tribochemical reaction products formed while sliding silicon oxide surfaces in the presence of adsorbed alcohol molecules in equilibrium with the vapor phase were studied. Wear and friction coefficient studies with varying contact loads and n-pentanol vapor environments were used to determine under what operating conditions the tribochemical reaction species was produced. Imaging time-of-flight secondary ion mass spectrometry and microinfrared spectroscopy found that hydrocarbon species with a molecular weight higher than the starting vapor molecules are produced when there is wear of the SiO(2) surface. When the n-pentanol vapor lubrication is effective and the silicon oxide surface does not wear, then the tribochemical polymerization products are negligible. These results imply that the tribochemical polymerization is associated with the substrate wear process occurring due to insufficient adsorbate supply or high mechanical load. The tribochemical reactions do not seem to be the primary lubrication mechanism for vapor phase lubrication of SiO(2) surfaces with alcohol, although they may lubricate the substrate momentarily upon failure of the alcohol vapor delivery to the sliding contact.

Theory of the influence of changes in salt concentration on the configuration of intrinsically curved, impenetrable, rod-like structures modeling DNA minicircles

DNA molecules in the familiar double helical B form are treated here as though they have rod-like structures obtained by stacking the nearly planar base pairs comprising them one on top of another with each rotated by approximately one-tenth of a full turn with respect to its immediate predecessor in the stack. As each base in a base pair is attached to the sugar–phosphate backbone chain of one of the two DNA strands that have come together to form the Watson–Crick structure, and each phosphate group in a backbone chain bears one electronic charge, two such charges are associated with each base pair. Thus, each base pair is subject to not only the elastic forces and moments exerted on it by its neighboring base pairs but also to electrostatic forces, of sequentially remote origin, that, because they are only partially screened out by positively charged counter ions, can render the molecule's equilibrium configurations sensitive to changes in the concentration of salt in the medium. As there are cases in which, even though the intramolecular electrostatic forces of repulsion are strong, the distance of closest approach has value equal to that of the impenetrable diameter of the molecule, the theory presented here takes into account self-contact. Examples are given of cases in which the theory predicts that the radius of gyration of the minimum energy configuration of a small (549 base pair) circularized DNA molecule (called a “DNA minicircle”) has a remarkably strong dependence on the salt concentration.

The dual descriptor to measure local reactivity on Buckminster fullerenes: an analysis within the framework of conceptual DFT

The Buckminster fullerene C₆₀ molecule was analyzed from the point of view of global and local reactivity. In particular, the dual descriptor--a local reactivity descriptor derived from conceptual density functional theory--was used to describe local reactivity in this molecule. One of the main advantages of using such a descriptor is the simplicity of obtaining accurate information about the local reactivity required to form covalent bonds without needing to perform calculations at higher levels of theory. The descriptor was adapted to the correct symmetry of this molecule in equilibrium so that the isosurface belongs to the totally symmetrical irreducible representation of the respective group of symmetry. Unlike global and some other local reactivity descriptors, correlation effects and basis sets are not critically important when using the dual descriptor because local reactivity is conserved at a qualitative level.