Charge Density Analysis of Ferulic Acid: Robustness of a Trifurcated C-H center dot center dot center dot O Hydrogen Bond

The toplogical features of a sporadic trifurcated C-H center dot center dot center dot O interaction region, where an oxygen atom acts as an acceptor of three weak hydrogen bonds, has been investigated by experimental and theoretical charge density analysis of ferulic acid. The interaction energy of the asymmetric molecular dimer formed by the trifurcated C-H center dot center dot center dot O motif, based on the multipolar model, is shown to be greater than the corresponding asymmetric O-H center dot center dot center dot O dimer in this crystal structure. Further, the hydrogen bond energies associated with these interaction motifs have been estimated from the local kinetic and potential energy densities at the bond critical points. The trends suggest that the interaction energy of the trifurcated C-H center dot center dot center dot O region is comparable to that of a single O-H center dot center dot center dot O hydrogen bond.

Electrophile-Induced C-C Bond Activation of Vinylcyclopropanes for the Synthesis of Z-Alkylidenetetrahydrofurans

We present a detailed study on the behavior of vinylcyclopropanes as masked donor acceptor system toward the stereoselective synthesis of Z-alkylidenetetrahydrofurans. Results of bromenium catalyzed indirect activation of C-C bond of vinylcyclopropanes and concomitant cyclization to alkylidenetetrahydrofuran and other heterocycles have been discussed. The stereoselective formation of the Z-isomer is strongly controlled by the extent of destabilization of one of the gauche conformers of the vinylcyclopropane. The ring-opening/cyclization step was found to be stereospecific as in the case of DA cyclopropanes. The activation of the C-C bond leads to a tight-carbocation intermediate, which is evident from the complete retention of the stereochemistry. The retention of configuration has been established by a necessary control experiment that rules out the possibility of a double inversion pathway. The present results serve as direct stereochemical evidence in support of a tight ion-pair intermediate versus the controversial S(N)2 pathway. A 2D potential energy scan has been carried out at B3LYP/6-31G(d) level theory to obtain the relative energies of the conformers. The Z-selectivity observed has been explained on the basis of the relative population of the conformers and modeling the intermediate and transition state involved in the reaction at M06-2x/6-31+G(d) level. Energy profile for the cyclization step was modeled considering various possible pathways through which cyclization can happen. The methodology has been successfully demonstrated on vinylcyclobutanes as well.

Dynamics of the North American continent

The forces that cause deformation of western North America have been debated for decades. Recent studies, primarily based on analysis of crustal stresses in the western United States, have suggested that the deformation of the region is mainly controlled by gravitational potential energy (GPE) variations and boundary loads, with basal tractions due to mantle flow playing a relatively minor role. We address these issues by modelling the deviatoric stress field over western North America from a 3-D finite element mantle circulation model with lateral viscosity variations. Our approach takes into account the contribution from both topography and shallow lithosphere structure (GPE) as well as that from deeper mantle flow in one single model, as opposed to separate lithosphere and circulation models, as has been done so far. In addition to predicting the deviatoric stresses we also jointly fit the constraints of geoid, dynamic topography and plate motion both globally and over North America, in order to ensure that the forces that arise in our models are dynamically consistent. We examine the sensitivity of the dynamic models to different lateral viscosity variations. We find that circulation models that include upper mantle slabs yield a better fit to observed plate velocities. Our results indicate that a model of GPE variations coupled with mantle convection gives the best fit to the observational constraints. We argue that although GPE variations control a large part of the deformation of the western United States, deeper mantle tractions also play a significant role. The average deviatoric stress magnitudes in the western United States range 30-40 MPa. The cratonic region exhibits higher coupling to mantle flow than the rest of the continent. We find that a relatively strong San Andreas fault gives a better fit to the observational constraints, especially that of plate velocity in western North America.

Nucleation of a Stable Solid from Melt in the Presence of Multiple Metastable Intermediate Phases: Wetting, Ostwald's Step Rule, and Vanishing Polymorphs

In many systems, nucleation of a stable solid may occur in the presence of other (often more than one) metastable phases. These may be polymorphic solids or even liquid phases. Sometimes, the metastable phase might have a lower free energy minimum than the liquid but higher than the stable-solid-phase minimum and have characteristics in between the parent liquid and the globally stable solid phase. In such cases, nucleation of the solid phase from the melt may be facilitated by the metastable phase because the latter can ``wet'' the interface between the parent and the daughter phases, even though there may be no signature of the existence of metastable phase in the thermodynamic properties of the parent liquid and the stable solid phase. Straightforward application of classical nucleation theory (CNT) is flawed here as it overestimates the nucleation barrier because surface tension is overestimated (by neglecting the metastable phases of intermediate order) while the thermodynamic free energy gap between daughter and parent phases remains unchanged. In this work, we discuss a density functional theory (DFT)-based statistical mechanical approach to explore and quantify such facilitation. We construct a simple order-parameter-dependent free energy surface that we then use in DFT to calculate (i) the order parameter profile, (ii) the overall nucleation free energy barrier, and (iii) the surface tension between the parent liquid and the metastable solid and also parent liquid and stable solid phases. The theory indeed finds that the nucleation free energy barrier can decrease significantly in the presence of wetting. This approach can provide a microscopic explanation of the Ostwald step rule and the well-known phenomenon of ``disappearing polymorphs'' that depends on temperature and other thermodynamic conditions. Theory reveals a diverse scenario for phase transformation kinetics, some of which may be explored via modem nanoscopic synthetic methods.

Thermal Decomposition of Propargyl Alcohol: Single Pulse Shock Tube Experimental and ab Initio Theoretical Study

Thermal decomposition of propargyl alcohol (C3H3OH), a molecule of interest in interstellar chemistry and combustion, was investigated using a single pulse shock tube in the temperature ranging from 953 to 1262 K. The products identified include acetylene, propyne, vinylacetylene, propynal, propenal, and benzene. The experimentally observed overall rate constant for thermal decomposition of propargyl alcohol was found to be k = 10((10.17 +/- 0.36)) exp(-39.70 +/- 1.83)/RT) s(-1) Ab initio theoretical calculations were carried out to understand the potential energy surfaces involved in the primary and secondary steps of propargyl alcohol thermal decomposition. Transition state theory was used to predict the rate constants, which were then used and refined in a kinetic simulation of the product profile. The first step in the decomposition is C-O bond dissociation, leading to the formation of two important radicals in combustion, OH and propargyl. This has been used to study the reverse OH propargyl radical reaction, about which there appears to be no prior work. Depending on the site of attack, this reaction leads to propargyl alcohol or propenal, one of the major products at temperatures below 1200 K. A detailed mechanism has been derived to explain all the observed products.

Composition dependent non-ideality in aqueous binary mixtures as a signature of avoided spinodal decomposition

We explore the potential energy landscape of structure breaking binary mixtures (SBBM) where two constituents dislike each other, yet remain macroscopically homogeneous at intermediate to high temperatures. Interestingly, we find that the origin of strong composition dependent non-ideal behaviour lies in its phase separated inherent structure. The inherent structure (IS) of SBBM exhibits bi-continuous phase as is usually formed during spinodal decomposition. We draw analogy of this correlation between non-ideality and phase separation in IS to explain observation of non-ideality in real aqueous mixtures of small amphiphilic solutes, containing both hydrophilic and hydrophobic groups. Although we have not been able to obtain IS of these liquids, we find that even at room temperature these liquids sustain formation of fluctuating, transient bi-continuous phase, with limited lifetime (tau less than or similar to 20 ps). While in the model (A, B) binary mixture, the non-ideal composition dependence can be considered as a fluctuation from a phase separated state, a similar scenario is expected to be responsible for the unusually strong non-ideality in these aqueous binary mixtures.

Unusual Fragility and Cooperativity in Glass-Forming and Crystalline PVDF/PMMA Blends in the Presence of Multiwall Carbon Nanotubes

Poly(vinylidene fluoride) (PVDF) and poly(methyl methacrylate) (PMMA) are completely miscible below 50 wt % PVDF in the blends. In this work, an attempt was made to understand the fragility/cooperativity relation in glass-forming and crystalline blends of PVDF/PMMA and in the presence of a heteronucleating agent, multiwall carbon nanotubes (CNTs). Hence, three representative blends were chosen: a completely amorphous (10/90 by wt, PVDF/PMMA), on the verge of amorphous miscibility (50/50 by wt, PVDF/PMMA), and crystalline (60/40 by wt, PVDF/PMMA) blends. The intermolecular cooperativity/coupling, fragility, and configurational entropy near the glass transition temperature (T-g) were studied using differential scanning calorimetry (DSC) and broadband dielectric relaxation spectroscopy (DRS). It was observed that the blends with higher concentration of PMMA were more fragile (fragility index m = 141) and those with higher concentration of PVDF were more strong (m = 78). Interestingly, the coupling was less in the glass-forming blends (10/90 by wt, PVDF/PMMA) than the crystalline blends as manifested from DRS. This observation was also supported by DSC measurements which reflected that the cooperative rearranging region (CRR) existed over a smaller length scales in fragile blends as compared to strong blends, possibly due to restricted amorphous mobility. This effect was more prominent in the presence of CNTs, in particular for 50/50 (by wt) and 60/40 (by wt) PVDF/PMMA blends. Further, the configurational entropy, as manifested from DRS, decreased significantly in the strong blends in striking contrast to the fragile blends, supported by DSC, which manifested in an increase in the volume of cooperativity in the strong blends. The higher coupling in the crystalline blends can be attributed to good packing of the amorphous regions. While this is understood for crystalline blends (60/40 by wt, PVDF/PMMA), it is envisaged that enhanced dynamic heterogeneity is accountable for increased coupling in the case of blends which are on the verge of amorphous miscibility (50/50 by wt, PVDF/PMMA). The latter is also supported by broad relaxations near the T-g in DRS. Interestingly, the intermolecular coupling in the blends in the presence of CNTs has reduced, though the potential energy barrier hindering the rearrangement of CRR is lower than the blends without CNTs. In addition, the amorphous packing is not as effective as the blends without CNTs. This is manifested from reduced volume of cooperativity in particular, for 50/50 (by wt) and 60/40 (by wt) blends.

Microwave Spectrum of Hexafluoroisopropanol and Torsional Behavior of Molecules with a CF3-C-CF3 Group

This paper presents the first microwave spectroscopic investigation on hexafluoroisopropanol (HFIP). A pulsed nozzle Fourier transform microwave spectrometer has been used to determine the rotational constants for HFIP as A = 2105.12166(18) MHz, B = 1053.99503(12) MHz, and C = 932.33959(13) MHz. In addition, five isotopologues of HFIP have been observed experimentally to determine the accurate structure of HFIP. The observed spectrum could be assigned to the most stable conformer of HFIP, called antiperiplanar. Available spectroscopic information and ab initio calculations on five prototype molecules helped in exploring the torsional behavior of molecules having a CF3-C-CF3 group. Two-dimensional potential energy surfaces have been analyzed for all molecules, which explained the presence/absence of doubling in the rotational transitions. With the help of natural bond orbital (NBO) analysis, reasons for the conformational preference of HFIP have been explained.

Microwave spectroscopic and theoretical investigations of the strongly hydrogen bonded hexafluoroisopropanol...water complex

This paper reports microwave spectroscopic and theoretical investigations on the interaction of water with hexafluoroisopropanol (HFIP). The HFIP monomer can exist in two conformations, antiperiplanar (AP) and synclinical (SC). The former is about 5 kJ mol(-1) more stable than the latter. Theoretical calculations predicted three potential minima for the complex, two having AP and one having SC conformations. Though, the binding energy for the HFIP(SC)...H2O turned out to be larger than that for the other two conformers having HFIP in the AP form, the global minimum for the complex in the potential energy hypersurface had HFIP in the AP form. Experimental rotational constants for four isotopologues measured using a pulsed nozzle Fourier transform microwave spectrometer, correspond to the global minimum in the potential energy hypersurface. The structural parameters and the internal dynamics of the complex could be determined from the rotational spectra of the four isotopologues. The global minimum has the HFIP(AP) as a hydrogen bond donor forming a strong hydrogen bond with H2O. To characterize the strength of the bonding and to probe the other interactions within the complex, atoms in molecules, non-covalent interaction index and natural bond orbital theoretical analyses have been performed.

Prediction of electronically nonadiabatic decomposition mechanisms of isolated gas phase nitrogen-rich energetic salt: Guanidium-triazolate

Electronically nonadiabatic decomposition pathways of guanidium triazolate are explored theoretically. Nonadiabatically coupled potential energy surfaces are explored at the complete active space self-consistent field (CASSCF) level of theory. For better estimation of energies complete active space second order perturbation theories (CASPT2 and CASMP2) are also employed. Density functional theory (DFT) with B3LYP functional and MP2 level of theory are used to explore subsequent ground state decomposition pathways. In comparison with all possible stable decomposition products (such as, N-2, NH3, HNC, HCN, NH2CN and CH3NC), only NH3 (with NH2CN) and N-2 are predicted to be energetically most accessible initial decomposition products. Furthermore, different conical intersections between the S-1 and S-0 surfaces, which are computed at the CASSCF(14,10)/6-31G(d) level of theory, are found to play an essential role in the excited state deactivation process of guanidium triazolate. This is the first report on the electronically nonadiabatic decomposition mechanisms of isolated guanidium triazolate salt. (C) 2015 Elsevier B.V. All rights reserved.

Triplet excited electronic state switching induced by hydrogen bonding: A transient absorption spectroscopy and time-dependent DFT study

The solvent plays a decisive role in the photochemistry and photophysics of aromatic ketones. Xanthone (XT) is one such aromatic ketone and its triplet-triplet (T-T) absorption spectra show intriguing solvatochromic behavior. Also, the reactivity of XT towards H-atom abstraction shows an unprecedented decrease in protic solvents relative to aprotic solvents. Therefore, a comprehensive solvatochromic analysis of the triplet-triplet absorption spectra of XT was carried out in conjunction with time dependent density functional theory using the ad hoc explicit solvent model approach. A detailed solvatochromic analysis of the T-T absorption bands of XT suggests that the hydrogen bonding interactions are different in the corresponding triplet excited states. Furthermore, the contributions of non-specific and hydrogen bonding interactions towards differential solvation of the triplet states in protic solvents were found to be of equal magnitude. The frontier molecular orbital and electron density difference analysis of the T-1 and T-2 states of XT indicates that the charge redistribution in these states leads to intermolecular hydrogen bond strengthening and weakening, respectively, relative to the S-0 state. This is further supported by the vertical excitation energy calculations of the XT-methanol supra-molecular complex. The intermolecular hydrogen bonding potential energy curves obtained for this complex in the S-0, T-1, and T-2 states support the model. In summary, we propose that the different hydrogen bonding mechanisms exhibited by the two lowest triplet excited states of XT result in a decreasing role of the n pi* triplet state, and are thus responsible for its reduced reactivity towards H-atom abstraction in protic solvents. (C) 2016 AIP Publishing LLC.

An extension of the Quasicontinuum Treatment of Multiscale Solid Systems to Nonzero Temperature

Covering the solid lattice with a finite-element mesh produces a coarse-grained system of mesh nodes as pseudoatoms interacting through an effective potential energy that depends implicitly on the thermodynamic state. Use of the pseudoatomic Hamiltonian in a Monte Carlo simulation of the two-dimensional Lennard-Jones crystal yields equilibrium thermomechanical properties (e.g., isotropic stress) in excellent agreement with ``exact'' fully atomistic results.

Component Assembling Model and Its Application to Quasi-Brittle Damage

Potential energy can be approximated by ‘‘pair-functional’’ potentials which is composed of pair potentials and embedding energy. Pair potentials are grouped according to discrete directions of atomic bonds such that each group is represented by an orientational component. Meanwhile, another kind of component, the volumetric one is derived from embedding energy. Damage and fracture are the changing and breaking of atomic bonds at the most fundamental level and have been reflected by the changing of these components’ properties. Therefore, material is treated as a component assembly, and its constitutive equations are formed by means of assembling these two kinds of components’ response functions. This material model is referred to as the component assembling model. Theoretical analysis and numerical computing indicate that the proposed model has the capacity of reproducing some results satisfactorily, with the advantages of physical explicitness and intrinsic induced anisotropy, etc.

Population of nonnative states of lysozyme variants drives amyloid fibril formation.

The propensity of protein molecules to self-assemble into highly ordered, fibrillar aggregates lies at the heart of understanding many disorders ranging from Alzheimer's disease to systemic lysozyme amyloidosis. In this paper we use highly accurate kinetic measurements of amyloid fibril growth in combination with spectroscopic tools to quantify the effect of modifications in solution conditions and in the amino acid sequence of human lysozyme on its propensity to form amyloid fibrils under acidic conditions. We elucidate and quantify the correlation between the rate of amyloid growth and the population of nonnative states, and we show that changes in amyloidogenicity are almost entirely due to alterations in the stability of the native state, while other regions of the global free-energy surface remain largely unmodified. These results provide insight into the complex dynamics of a macromolecule on a multidimensional energy landscape and point the way for a better understanding of amyloid diseases.

Computation of stress intensity factors by the sub-region mixed finite element method of lines

Based on the sub-region generalized variational principle, a sub-region mixed version of the newly-developed semi-analytical 'finite element method of lines' (FEMOL) is proposed in this paper for accurate and efficient computation of stress intensity factors (SIFs) of two-dimensional notches/cracks. The circular regions surrounding notch/crack tips are taken as the complementary energy region in which a number of leading terms of singular solutions for stresses are used, with the sought SIFs being among the unknown coefficients. The rest of the arbitrary domain is taken as the potential energy region in which FEMOL is applied to obtain approximate displacements. A mixed system of ordinary differential equations (ODEs) and algebraic equations is derived via the sub-region generalized variational principle. A singularity removal technique that eliminates the stress parameters from the mixed equation system eventually yields a standard FEMOL ODE system, the solution of which is no longer singular and is simply and efficiently obtained using a standard general-purpose ODE solver. A number of numerical examples, including bi-material notches/cracks in anti-plane and plane elasticity, are given to show the generally excellent performance of the proposed method.