Chem Phys Research Articles

Explicit Incorporation of Hard and Soft Protein-Protein Interactions into Models for Crowding Effects in Protein Mixtures. 2. Effects of Varying Hard and Soft Interactions upon Prototypical Chemical Equilibria.

Previously derived approximate analytical relations for the activity coefficient of each solute in a mixture of up to three spherical solutes in a highly nonideal solution interacting via square well potentials of mean force (Hoppe, T.; Minton, A. P. J Phys Chem B. 2016, 120, 11866-11872) were used to explore the effect of heterogeneity in volume occupancy and intermolecular interactions upon prototypical schemes representing solubility, partitioning, conformational isomerization, and self-association in crowded solutions. Results generally indicate that all of the equilibria explored are exquisitely sensitive to variations in both volume occupancy and intermolecular interaction and have important implications for the design and execution of more detailed simulations of complex media.

Carbonization of Silicon Nanoparticles via Ablation Induced by Femtosecond Laser Pulses in Hexane

Silicon carbide (SiC) has been widely used in various technological applications, including power devices, light-receiving devices, and light-emitting devices. Several methods for fabricating SiC particles with nanometer dimensions have been reported, including carbo-thermal reduction of silica, chemical vapor deposition, laser pyrolysis, and microwave irradiation. To develop a new and simple method for fabricating SiC nanoparticles, we investigated the possibility of using femtosecond-laser ablation. In this paper, we report the formation of SiC nanoparticles by femtosecond-laser ablation on silicon immersed in hexane. By using a high-peak-power laser that can achieve extremely high temperatures and pressures on the silicon surface, SiC nanoparticles were successfully fabricated via ablation in hexane. In our experiments, femtosecond pulses from a Yb-fiber laser were used to irradiate to silicon single crystal. The laser was focused onto a spot on the silicon surface. After ablation, we evaluated the particles on the target substrate and particles in the irradiated hexane. Scanning electron microscopy revealed that the particles range in size from 100 to 400 nm. X-ray diffraction analysis indicated that the nanoparticles might be SiC. The characteristic X-ray photoelectron spectroscopy peaks of nanoparticles were Si-2p (100.1 eV) and C-1s (282.9 eV), which are identical to the characteristic peaks of SiC (John et al. in Handbook of X-ray photoelectron spectroscopy, Physical Electronics, Eden Prairie, 1995; Hijikata et al. in Appl Surf Sci 184:161–166, 2001; Shen et al. in Chem Phys Lett 375:177–184, 2003). We also used transmission electron microscopy and electron energy-loss spectroscopy to evaluate particles from the irradiated hexane. Such a simple method of fabricating SiC nanoparticles by femtosecond-laser ablation may open new possibilities in the development of growth techniques for SiC.

Effect of strontium inclusion on the bioactivity of phosphate-based glasses

We have conducted first-principles and classical molecular dynamics simulations of various compositions of strontium-containing phosphate glasses, to understand how strontium incorporation will change the glasses’ activity when implanted into the body (bioactivity). To perform the classical simulations, we have developed a new interatomic potential, which takes account of the polarizability of the oxygen ions. The Sr–O bond length is ∼2.44–2.49 Å, and the coordination number is 7.5–7.8. The Qn distribution and network connectivity were roughly constant for these compositions. Sr bonds to a similar number of phosphate chains as Ca does; based on our previous work (Christie et al. in J Phys Chem B 117:10652, 2013), this implies that SrO ↔ CaO substitution will barely change the dissolution rate of these glasses and that the bioactivity will remain essentially constant. Strontium could therefore be incorporated into phosphate glass for biomedical applications.

DFT and TD-DFT study of the enol and thiol tautomers of 3-thioxopropanal in the ground and first singlet excited states

In the first part of this paper, a comprehensive theoretical study of molecular structure, stability, intramolecular hydrogen bond (IMHB) and [Formula: see text]-electron delocalization ([Formula: see text]-ED) of the enol and thiol tautomers of 3-thioxopropanal (TPA) in the ground state is performed. In this regard, all of the plausible conformations of TPA at M06-2X/6-311[Formula: see text]G(d,p) are optimized and a variety of theoretical levels are employed to identify the global minimum. Our calculations show that E1 is the most stable form that is in contrast to the results of Gonzalez et al. [J Phys Chem 101: 9710, 1997]. In order to elucidate this duality, the IMHB and [Formula: see text]-ED of chelated forms (E1 and T1) have been extensively investigated. So, it is found that both of the IMHB analysis and [Formula: see text]-ED concepts emphasize on the E1, as the global minimum. In the second part of this study, a set of simple electron-withdrawing and electron-donating substituents such as CN, F, Cl, CH3 and NH2 have been considered to evaluate their effects on the IMHB of the first singlet excited state of E1 and T1 at TD-DFT/6–311[Formula: see text]G(d,p) level of theory. According to our analysis, it was found that the IMHB strength of the excited states are much weaker than the ground states. Surprisingly, the IMHB of thiol derivatives is stronger than the enol ones in contrast to the ground state. Furthermore, the substitution effects in the ground and excited states are significantly different. Finally, various linear correlations between the IMHB energies with geometrical, topological and molecular orbital parameters are obtained.

Minimizing irreversible losses in quantum systems by local counterdiabatic driving

Counterdiabatic driving protocols have been proposed [Demirplak M, Rice SA (2003) J Chem Phys A 107:9937-9945; Berry M (2009) J Phys A Math Theor 42:365303] as a means to make fast changes in the Hamiltonian without exciting transitions. Such driving in principle allows one to realize arbitrarily fast annealing protocols or implement fast dissipationless driving, circumventing standard adiabatic limitations requiring infinitesimally slow rates. These ideas were tested and used both experimentally and theoretically in small systems, but in larger chaotic systems, it is known that exact counterdiabatic protocols do not exist. In this work, we develop a simple variational approach allowing one to find the best possible counterdiabatic protocols given physical constraints, like locality. These protocols are easy to derive and implement both experimentally and numerically. We show that, using these approximate protocols, one can drastically suppress heating and increase fidelity of quantum annealing protocols in complex many-particle systems. In the fast limit, these protocols provide an effective dual description of adiabatic dynamics, where the coupling constant plays the role of time and the counterdiabatic term plays the role of the Hamiltonian.

Microencapsulation thermodynamics of methylated β-cyclodextrins with bile salt: enthalpy, entropy, and solvent effect

The interactions between bile salts and modified cyclodextrins (CD) have aroused intensive interest because of their influence on the in vivo drug release within the small intestine. We use a recently proposed molecular dynamics/quantum mechanics/continuum solvent model (Ye et al. in Chem Phys Lett 648:170, 2016) to investigate the microscopic binding mechanisms of the natural, dimethylated (M200), randomly methylated (M214), and trimethylated (M300) $$\beta$$ -CDs, with glycocholate (GC). The computed binding free energies of the four CDs with GC decrease in the following order: natural $$\beta$$ -CD > M200 > M214 > M300, which is in accord with the experimental data. As suggested by the computed thermodynamic quantities, the relative stabilities of the four CD/GC complexes are determined by both the host–guest interactions (enthalpy plus entropy) and the solvent effects. Moreover, the former favors M200, while the latter favors natural $$\beta$$ -CD. For M300, both factors are in disadvantage.

Excited state electron affinity calculations for aluminum

Excited states of negative aluminum ion are reviewed, and calculations of electron affinities of the states $$(3s^23p^2)^1D$$ and $$(3s3p^3){^5}{S}{^\circ }$$ relative to the $$(3s^23p)^2P^\circ$$ and $$(3s3p^2)^4P$$ respectively of the neutral aluminum atom are reported in the framework of nonrelativistic configuration interaction (CI) method. A priori selected CI (SCI) with truncation energy error (Bunge in J Chem Phys 125:014107, 2006) and CI by parts (Bunge and Carbo-Dorca in J Chem Phys 125:014108, 2006) are used to approximate the valence nonrelativistic energy. Systematic studies of convergence of electron affinity with respect to the CI excitation level are reported. The calculated value of the electron affinity for $$^1D$$ state is 78.675(3) meV. Detailed Calculations on the $$^5S^\circ$$ state reveals that is 1216.8166(3) meV below the $$^4P$$ state.

Pulse/Pulse-Reverse Electrodeposition of Copper Electrocatalysts for CO2 Reduction to Ethylene

There have been many attempts to find efficient approaches to reduce CO2 to various organic compounds due to the industrial need for a carbon source and the general need to mitigate the large amounts of CO2 generated by human activities. However, a recent DOE report indicates that major scientific challenges still exist to realize development of an efficient, inexpensive, and durable catalytic system that efficiently facilitates complex, multi-electron and atom/ion transfer events [[1]]. Modern carbon emission mitigation efforts have focused primarily on carbon capture and sequestration (CCS) [[2]]. Despite challenges extant in developing technologies for CO2 conversion to value-added products, such capabilities are anticipated to reduce risk and offset the cost of CCS development and thus encourage broader industrial adoption of CO2 mitigation processes. Recent work toward development of efficient, selective, and active copper electrocatalysts for reduction of CO2 to ethylene is presented. Copper is well known as a unique CO2 reduction electrocatalyst, capable of forming alcohol (e.g., ethanol) and hydrocarbon (e.g., methane, ethylene) products in addition to aldehydes, carboxylic acids, carbon monoxide and hydrogen [[3],[4]]. Ethylene is of specific interest, as its role as a platform feedstock for the chemicals and plastics industries affords it an appreciably higher market value than many other potential products [[5]]. However, the catalytic activity and selectivity achieved to date with Cu catalysts and CO2-saturated aqueous carbonate solutions have not been sufficient to enable development of an industrially viable process. Faraday and MIT are currently investigating pulse/pulse-reverse electrodeposition methods as a means to fabricate copper catalysts with greater activity and ethylene selectivity in order to enable large-scale electrocatalytic conversion of CO2. The microstructure of metallic catalysts is known to influence various properties including selectivity and activity; for copper in particular, a strong effect on the selectivity for ethylene versus methane as a function of crystallographic orientation has been reported [[6],[7]]. Given that pulsed electrodeposition is known to have a significant effect on the microstructure of the resulting metal films [[8],[9]], the technology is a natural candidate for fabrication of novel, high-performance copper CO2 reduction catalysts. In this work, catalyst activity and selectivity were further enhanced through the use of a modified literature activation protocol involving aerobic thermal oxidation followed by electrochemical reduction [[10]]. Photographs of a representative catalyst coupon at each stage of fabrication are presented in Figure 1. This talk will present data confirming that catalytic properties can be enhanced by tuning both the pulsed waveform used for deposition as well as the conditions used in the oxidation/reduction activation protocol. We are focusing development toward the use of aqueous solutions containing CO2-solubilizing additives such as room-temperature ionic liquids and cyclic amines. These materials have been extensively studied as a liquid-phase capture media for removing CO2 from post-combustion exhaust streams (e.g., power plants) [[11],[12]], and have the potential to increase the effective CO2 concentration at catalyst active sites and thus enhance the faradaic efficiency of the CO2 reduction reaction relative to H2 formation from water electrolysis. There are advantages to developing an advanced technology for electrocatalytic conversion of CO2 using capture media already in large-scale industrial use, since it would dramatically reduce the logistical and economic costs of integration into existing facilities. The data gathered to date provide encouraging evidence that enhanced catalytic performance can be realized through the use of such CO2-solubilizing additives in tandem with pulse-deposited copper electrocatalysts. The authors acknowledge the financial support of NASA Contract NNX14CC53P and US DOE Contract DE-SC0015812. References [[1]] Basic Research Needs: Catalysis for Energy, 8/6-8/2007. www.sc.doe.gov/bes/reports/list.html [[2]] Carbon Dioxide Capture and Sequestration. http://www3.epa.gov/climatechange/ccs/ [[3]] Y. Hori. “Electrochemical CO2 reduction on metal electrodes.” Modern Aspects of Electrochemistry, 42, C. Vayenas, Ed. New York: Springer (2008). [[4]] Chaplin, R., Wragg, A.A.; J. Appl. Electrochem.(2003), 33, 1107. [[5]] S. Verma et al. ChemSusChem 9: 1972 (2016). [[6]] Y. Hori et al. J Phys Chem B 106: 15 (2002). [[7]] K.W. Frese, Jr. “Electrochemical Reduction of CO2 at Solid Electrodes.” Electrochemical and Electrocatalytic Reactions of Carbon Dioxide, B.P. Sullivan et al., eds. Amsterdam: Elsevier, pp. 145 (1993). [[8]] E.J. Taylor, J.J. Sun. U.S. Patent 8,603,315, 12/10/2013. [[9]] A.C. Mishra et al. J Mater Sci 44(13): 3520 (2009). [[10]] C.W. Li, M.W. Kanan. J Am Chem Soc 134: 7231 (2012). [[11]] J.D. Figueroa et al. Int J Greenhouse Gas Control 2(1): 9 (2008). [[12]] J. Anthony, J. Carroll, DOE NETL, Aug 2016. https://www.netl.doe.gov/File%20Library/Events/2016/c02%20cap%20review/1-Monday/J-Anthony-SouthernCo-Testing-at-National-Carbon-Capture-Center.pdf Figure 1

Pressure dependence of viscosity in supercooled water and a unified approach for thermodynamic and dynamic anomalies of water

The anomalous decrease of the viscosity of water with applied pressure has been known for over a century. It occurs concurrently with major structural changes: The second coordination shell around a molecule collapses onto the first shell. Viscosity is thus a macroscopic witness of the progressive breaking of the tetrahedral hydrogen bond network that makes water so peculiar. At low temperature, water at ambient pressure becomes more tetrahedral and the effect of pressure becomes stronger. However, surprisingly, no data are available for the viscosity of supercooled water under pressure, in which dramatic anomalies are expected based on interpolation between ambient pressure data for supercooled water and high pressure data for stable water. Here we report measurements with a time-of-flight viscometer down to [Formula: see text] and up to [Formula: see text], revealing a reduction of viscosity by pressure by as much as 42%. Inspired by a previous attempt [Tanaka H (2000) J Chem Phys 112:799-809], we show that a remarkably simple extension of a two-state model [Holten V, Sengers JV, Anisimov MA (2014) J Phys Chem Ref Data 43:043101], initially developed to reproduce thermodynamic properties, is able to accurately describe dynamic properties (viscosity, self-diffusion coefficient, and rotational correlation time) as well. Our results support the idea that water is a mixture of a high density, "fragile" liquid, and a low density, "strong" liquid, the varying proportion of which explains the anomalies and fragile-to-strong crossover in water.

The emission spectroscopy of AlD in the visible region: experimental and theoretical investigations

The emission spectrum of the AlD isotopologue has been experimentally studied using Fourier transform spectroscopy in the 17,700−28,500 cm−1 spectral region. AlD molecules were produced within an aluminum hollow-cathode lamp with two anodes in the presence of 2.7 Torr of Ne and 0.2 Torr of ND3. The observed bands have been assigned to the A 1Π− X 1Σ+ (0−0,1 and 1−0,1,2,3 bands) and C 1Σ+− A 1Π (0−0 and 1−1 bands) transitions. In total, more than 450 rotational frequencies were measured with an absolute accuracy of about 0.002cm−1. The current data have been combined with available measurements of the pure rotational lines by Halfen and Ziurys [Astrophys J 2010; 713: 520-523] and with the ro-vibrational bands by White et al. [J Chem Phys 1993;99:8371-8378] to provide improved spectroscopic constants of the X 1Σ+, A 1Π and C 1Σ+ states of AlD. These results match closely theoretical values obtained using a new set of ab initio potentials calculated with a spin-orbit Hamiltonian.

Hirshfeld partitioning from non-extensive entropies

We show that the statistical divergence measures associated with non-extensive thermodynamic entropy functions—specifically the Tsallis, Reyni, Sharma–Mittal, supraextensive, and H-divergences—are associated with the Hirshfeld atoms-in-molecules partitioning. This extends the treatment of Nalewajski and Parr (J Phys Chem A 109:3957–3959, 2005), (for the extensive Shannon entropy) to non-extensive entropy measures. It also extends the work of Heidar-Zadeh and Ayers (J Chem Phys 142(4):044107, 2015), (for divergence measures that are local density functionals) to non-local functionals. These results dramatically extend the mathematical framework that one can use for similarity-based atoms-in-molecules partitioning.

Excited Rotational States in Doped $${^{4}}$$ 4 He Clusters: a Diffusion Monte Carlo Analysis

We report an extension of diffusion Monte Carlo (DMC) to the calculation of the molecular rotational energies by means of the generalized, symmetry-adapted, imaginary-time correlation functions (SAITCFs) originally introduced in the reptation quantum Monte Carlo (RQMC) framework (Skrbic in J Phys Chem A 111:12749, 2007). We studied the a-type and b-type rotational lines of the CO( $$^{4}$$ He) $$_{N}$$ clusters with $$N=$$ 1–8 that correlate, in the dimer limit, with the end-over-end and free-rotor transitions. We compare the SAITCF–DMC results with accurate DVR (for the dimer case), RQMC and other DMC data, and with reference experimental findings (Surin in Phys Rev Lett 101:233401, 2008). A good agreement is generally found, but a systematic underestimation of the SAITCF–DMC rotational energies of the b-type series is observed. Sources of inaccuracy in our theoretical approach and in the computational protocol are discussed and analyzed in detail.

A simple algorithm for the calculation of an approximate electrophoretic mobility of a spherical colloidal particle based on the modified Poisson-Boltzmann equation

A simple algorithm is presented for the calculation of an approximate electrophoretic mobility of a spherical colloidal particle in an electrolyte solution. The obtained expressions are based on an approximate form of the modified Poisson-Boltzmann equation taking into account the ion size effects through Carnahan-Starling activity coefficients of electrolyte ions (J Chem Phys 51:635,31). Agreement with the exact numerical results by Lopez-Garcia et al. (J Colloid Interface Sci 458:273,27) is good for most practical cases.

Strain in strain-free benzenoid hydrocarbons: the case of fibonacenes

In a recent paper (Radenkovic et al. Chem Phys Lett 625:69–72, 2015), a new method for quantifying the strain energy in benzenoid molecules, resulting from the repulsion between the bay H-atoms was elaborated. In this work, we present a modified procedure, capable of estimating the strain energy in a single-step calculation. Strain energies were obtained at the B3LYP/def2-TZVP level of density functional theory. It was found that in benzenoid molecules with a single bay region, the strain energy is essentially constant, equal to around 7.3 kJ/mol. On the other hand, in the case of the first four members of the fibonacene series, the strain energy is found to be linearly proportional to the number of bay regions.

Molecular Insights into Biomolecular Structure and Dynamics by 14N NMR

The structural and dynamic analysis of proteins by NMR in the solid-state has typically required extensive isotope labelling. Here we report our progress using the naturally occurring isotopes 1H and 14N to probe the structure and dynamics of biomolecules. Employing indirect-detection methods, we have previously demonstrated the feasibility of characterising the quadrupolar interaction present at the naturally occurring 14N sites within proteins using 13C as a ‘spy’ nucleus (Jarvis, 2013). These methods demonstrated that in well folded proteins, limited dynamic averaging of the quadrupolar interaction occurred and the magnitude of the quadrupolar interaction reflected the nature of the hydrogen bonding experienced by the nitrogen, with differences of up to 200 kHz measured between amides in alpha helices and beta sheets - allowing a detailed analysis of the electronic environment along the protein backbone. We have extended this methodology to exploit protons as a spy nucleus, where significant enhancements in sensitivity are realised. These advances have opened up the possibility of conducting a molecular analysis of unlabelled biomolecules such as ex-vivo or environmental samples. Currently, we are applying these methods to amyloid fibres, to provide insights into their backbone conformation and polymorphism.Jarvis, J.A., Haies, I.M., et al., An efficient NMR method for the characterisation of 14N sites through indirect 13C detection. Phys Chem Chem Phys, 2013. 15(20): p. 7613-20.

Computational Characterization of Oligomerization of FVFLM Peptide and its Ability to Inhibit Beta Amyloid Aggregation

Preeclampsia, a pregnancy-specific disorder, shares typical pathophysiological features with protein misfolding disorders including Alzheimer's disease1. Characteristic for preeclampsia is the involvement of multiple proteins of which fragments of SERPINA1 and β-amyloid co-aggregate in urine and placenta of preeclamptic women. This work explores the biophysical basis of this interaction by investigating the multidimensional efficacy of the FVFLM sequence in SERPINA1, as a model inhibitory agent of β-amyloid aggregation. Several algorithms predict FVFLM peptide as being a highly amyloidogenic2,3. After studying the oligomerization of FVFLM peptides using all-atom molecular dynamics simulations with the GROMOS43a1 force field and explicit water, we report that FVFLM can aggregate and its aggregation is spontaneous with a remarkably faster rate than that recorded for KLVFF (aggregation “hot-spot” from β-amyloid). The population of fibril-prone conformations in the monomeric state of KLVFF was found to be lower than FVFLM indicating the faster aggregation process of FVFLM4. The fast kinetics of FVFLM aggregation was found to be driven primarily by core-like aromatic interactions originating from the anti-parallel orientation of complementarily uncharged strands. We also demonstrate a high propensity of FVFLM for KLVFF binding. When present, FVFLM disrupts the β-amyloid aggregation pathway and we propose that FVFLM-like peptides might be used to prevent the assembly of full-length Aβ or other pro-amyloidogenic peptides into amyloid fibrils.1. Buhimschi, I.A. et al. Protein misfolding, congophilia, oligomerization, and defective amyloid processing in preeclampsia. Science translational medicine6, 245ra292 (2014).2. Zambrano, R. et al. AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures. Nucleic Acids Res (2015).3. Kouza, M., Faraggi, E., Kolinski, A. & Kloczkowski, A. in Prediction of Protein Secondary Structure, Vol. 1484. (eds. Y. Zhou, A. Kloczkowski, E. Faraggi & Y. Yang) 7-24 (Humana Press, New York; 2016).4. Nam, H.B., Kouza, M., Hoang, Z. & Li, M.S. Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: Insights from all-atom simulations. J Chem Phys 132, 165104 (2010)

A theoretical assignment on excited‐state intramolecular proton transfer mechanism for quercetin

AbstractIn the present work, we investigate a new chromophore (ie, quercetin) (Simkovitch et al J Phys Chem B 119 [2015] 10244) about its complex excited‐state intramolecular proton transfer (ESIPT) process based on density functional theory and time‐dependent density functional theory methods. On the basis of the calculation of electron density ρ(r) and Laplacian ∇2ρ(r) at the bond critical point using atoms‐in‐molecule theory, the intramolecular hydrogen bonds (O1‐H2⋯O5 and O3‐H4⋯O5) have been supported to be formed in the S0 state. Comparing the prime structural variations of quercetin involved in its 2 intramolecular hydrogen bonds, we find that these 2 hydrogen bonds should be strengthened in the S1 state, which is a fundamental precondition for facilitating the ESIPT process. Concomitantly, infrared vibrational spectra analysis further verifies this viewpoint. In good agreement with previous experimental spectra results, we find that quercetin reveals 2 kinds of excited‐state structures (quercetin* and quercetin‐PT1*) in the S1 state. Frontier molecular orbitals depict the nature of electronically excited state and support the ESIPT reaction. Our scanned potential energy curves according to variational O1‐H2 and O3‐H4 coordinates demonstrate that the proton transfer process should be more likely to occur in the S1 state via hydrogen bond wire O1‐H2⋯O5 rather than O3‐H4⋯O5 because of the lower potential energy barrier 2.3 kcal/mol. Our present work explains previous experimental result and makes up the deficiency of mechanism in previous experiment. In the end, we make a reasonable assignment for ESIPT process of quercetin.

Correlation effects on the interelectronic distributions of localized electron pairs

It has been shown previously that a wealth of chemical insight may be drawn from studying the interelectronic distribution function for localized electron pairs within a molecular system (Hennessey et al. in Phys Chem Chem Phys 16(46):25548–25556, 2014); however, these accounts have been limited due to the relative inaccuracy of the underlying Hartree–Fock electronic structure model that has been employed. In the current work, we study how the interelectronic distribution function of single electron pairs, represented by localized molecular orbitals, changes between a Hartree–Fock and density functional electronic structure model. We find that localized electron pairs expand, relative to a Hartree–Fock model, in a small but significant way when modelled with density functional theory. More specifically, we generally find that compact electron pairs (i.e. those pairs having narrow distribution functions near small interelectronic distances) result in a smaller change due to correlation than electron pairs more broadly distributed. This counterintuitive effect is attributed to the fact that compact electron pairs are generally held close together by a relatively rigid confining potential (i.e. attraction from local nuclei and repulsion from neighbouring electrons). However, in cases where a series of species all have nearly identical nuclear structure in the vicinity of the LMO of interest, more compact electron pairs did in fact experience the greatest change in interelectronic separation and electron repulsion upon the incorporation of a correlated model. Also, if one allows the geometry of the molecular species to relax, bonds associated with LMOs having compact interelectronic distributions tend to elongate the most with a correlated model (relative to Hartree–Fock) and the resultant deformation of the interelectronic distribution functions then show the most significant changes due to correlation. The results presented herein demonstrate the utility of Kohn–Sham density functional theory for the description of localized chemical space within the scope of the localized pair model.

Macromolecular Origins of Fifth Shear Stress Harmonic in Large-Amplitude Oscillatory Shear Flow

This study examines the simplest relevant molecular model of a polymeric liquid in large-amplitude oscillatory shear (LAOS) flow: the suspension of rigid dumbbells in a Newtonian solvent. For such suspensions, the viscoelastic response of the polymeric liquid depends exclusively on the dynamics of dumbbell orientation. We have previously derived explicit analytical expressions for the shear rate amplitude and frequency dependences of the first and third harmonics of the alternating shear stress response in LAOS. Higher harmonics sculpt the shear stress, distorting it from its sinusoidal shape. In this work, we derive the polymer contribution to the shear stress response up to and including the next higher, fifth harmonic. For this, we use the fourth order term in the expansion of the orientation distribution to calculate the shear stress response. Our analysis employs the general method of Bird and Armstrong [J Chem Phys, 56, 3680 (1972)]. Our expression is the only one to have been derived from a molecular theory for a fifth harmonic. Our paper thus provides the first glimpse of the molecular origins of a shear stress harmonic higher than the third.

Studying lowest energy structures of carbon clusters by bond-order empirical potentials

A very recently developed optimization algorithm for carbon clusters (C n s) (Yen and Lai J Chem Phys 142:084313, 2015) is combined separately with different empirical bond-order potentials which were proposed also for carbon materials, and they are applied to calculate the lowest energy structures of C n s studying their structural changes at different size n. Based on predicted structures, we evaluate the practicality of four analytic bond-order empirical potentials, namely the Tersoff, Tersoff–Erhart–Albe, first-generation Brenner and second-generation Brenner (SGB) potentials. Generally, we found that the cluster C n (n = 3–60) obtained by the SGB potential undergoes a series of dramatic structural transitions, i.e., from a linear → a single ring → a multi-ring/quasi-two-dimensional bowl-like → three-dimensional fullerene-like shape; such variability of structural forms was not seen in the other three potentials. On closer examination of the C n s calculated using this potential and further comparing them with those obtained by the semiempirical density functional tight-binding theory calculations, we found that these C n are more realistic than similar works reported in the literature. In this respect, due to its potential applications in the study of chemically complex systems of different atoms especially chemical reactions (Che et al. Theor Chem Acc 102:346, 1999), the SGB potential can, moreover, be used to investigate larger size C n , and calculated structural results by this potential are naturally input configurations for higher-level density functional theory calculations. Another most remarkable finding in the present work is the C n results calculated by Tersoff–Erhart–Albe empirical potential. It predicts a two-dimensional development of graphene structure, exhibiting always a zigzag edge in the optimized clusters. This empirical potential can thus be applied to study graphene-related materials such as that shown in a recent paper (Yoon et al. J Chem Phys 139:204702, 2013).