Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method

The first derivative of the total energy with respect to nuclear coordinates (the energy gradient) in the fragment molecular orbital (FMO) method is applied to second order M?ller-Plesset perturbation theory (MP2), resulting in the analytic derivative of the correlation energy in the external self-consistent electrostatic field. The completely analytic energy gradient equations are formulated at the FMO-MP2 level. Both for molecular clusters (H(2)O)(64) and a system with fragmentation across covalent bonds, a capped alanine decamer, the analytic FMO-MP2 energy gradients with the electrostatic dimer approximation are shown to be complete and accurate by comparing them with the corresponding numeric gradients. The developed gradient is parallelized with the parallel efficiency of about 97% on 32 Pentium4 nodes connected by Gigabit Ethernet.     

Computation of some thermodynamic properties of helium–neon and helium–krypton fluid mixtures using molecular dynamics simulation

We have performed molecular dynamics simulations to obtain internal energy and pressure of helium–neon and helium–krypton mixtures at different densities using accurate recently two-body ab initio potentials supplemented by quantum corrections following the Feynman–Hibbs approach. The significance of this work is that the three-body expression of Wang and Sadus [22] was used to improve prediction of the pressures and internal energies of helium + krypton and helium + neon mixtures without requiring an expensive three-body calculation. Our results show a good agreement with the corresponding experimental data.     

Effect of pressure on the structure and dynamics of hydrogen bonds in ethylene glycol–water mixtures: Numerical simulation data

Water?ethylene glycol mixtures containing from 0.002 to 0.998 mole fractions of ethylene glycol at T = 298.15 K and P = 0.1 and 100 MPa are simulated by means of classical molecular dynamics. Such structural and dynamic characteristics of hydrogen bonds as the average number and lifetime, along with the distribution of molecules over the number of hydrogen bonds, are calculated; their changes are analyzed, depending on the mixture’s composition and pressure. It is shown that the components are characterized by a high degree of interpenetration and form a uniform infinite hydrogen-bonded cluster over the range of concentrations. It is found that the higher the concentration of ethylene glycol, the greater the stability of all hydrogen bonds. It is concluded that an increase in pressure lowers the number of hydrogen bonds, while the average lifetime of the remaining hydrogen bonds grows.     

Comparison of two quantitative GC–MS methods for analysis of tomato aroma based on purge-and-trap and on solid-phase microextraction

Two analytical procedures, one based on purge-and-trap and the other on solid phase microextraction, both followed by GC–MS measurement using an ion-trap mass spectrometer in the electron impact mode, have been developed for determination and quantitation of up to 39 aroma compounds in fresh tomatoes. The method based on purge-and-trap for isolation of the volatile compounds uses Tenax as adsorbent and a hexane–diethyl ether mixture as solvent for elution. The method was validated for linearity, precision (better than 20% for most compounds), and limit of detection, which was approximately 1 ng g⁻¹. This method enabled identification of up to 30 compounds in real samples. Use of SPME was considered as an alternative, to simplify sample treatment while maintaining the information level for the samples (e.g. the number of compounds detected) and quality of quantitation. A procedure based on SPME using a Carboxen/polydimethylsiloxane fibre was developed and validated for determination of 29 aroma compounds; precision was better than 20% and limits of detection ranged from 4 to 30 ng g⁻¹.     

Distributed memory parallel implementation of energies and gradients for second-order Møller-Plesset perturbation theory with the resolution-of-the-identity approximation

We present a parallel implementation of second-order M?ller-Plesset perturbation theory with the resolution-of-the-identity approximation (RI-MP2). The implementation is based on a recent improved sequential implementation of RI-MP2 within the Turbomole program package and employs the message passing interface (MPI) standard for communication between distributed memory nodes. The parallel implementation extends the applicability of canonical MP2 to considerably larger systems. Examples are presented for full geometry optimizations with up to 60 atoms and 3300 basis functions and MP2 energy calculations with more than 200 atoms and 7000 basis functions.     

Determination and measurement of solid–liquid equilibrium for binary fatty acid mixtures based on NRTL and UNIQUAC activity models

The estimation of solid–liquid phase equilibrium is important for the design, development, and operation of many industrial processes because of application in many manufacturing fields such as cosmetic, pharmaceutic, and biotechnology industries. In this work, we measured solid–liquid phase equilibrium of six fatty acid binary mixtures using the DSC technique and developed thermodynamic approaches for binary fatty acid mixtures to estimate melting temperatures as a function of mole fraction in solid–liquid phase equilibrium. Derivation of NRTL and UNIQUAC activity models was developed to predict melting temperatures and latent heat to achieve eutectic points of undecylic acid, pentadecylic acid, margaric acid, and stearic acid six pairwise binary mixtures. The fatty acids eutectic mixtures are appropriate for heat water systems, phase clothes, concrete, and other similar applications. The results showed low deviations from experimental data measured in this study.

     

Reconstruction and analysis of correlation networks based on GC–MS metabolomics data for young hypertensive men

The awareness, treatment, and control rates of hypertension for young adults are much lower than average. It is urgently needed to explore the variances of metabolic profiles for early diagnosis and treatment of hypertension. In current study, we applied a GC–MS based metabolomics platform coupled with a network approach to analyze plasma samples from young hypertensive men and age-matched healthy controls. Our findings confirmed distinct metabolic footprints of young hypertensive men. The significantly altered metabolites between two groups were enriched for the biological module of amino acids biosynthesis. The correlations of GC–MS metabolomics data were then visualized as networks based on Pearson correlation coefficient (threshold = 0.6). The plasma metabolites identified by GC–MS and the significantly altered metabolites (P < 0.05) between patients and controls were respectively included as nodes of a network. Statistical and topological characteristics of the networks were studied in detail. A few amino acids, glycine, lysine, and cystine, were screened as hub metabolites with higher values of degree (k), and also obtained highest scores of three centrality indices. The short average path lengths and high clustering coefficients of the networks revealed a small-world property, indicating that variances of these amino acids have a major impact on the metabolic change in young hypertensive men. These results suggested that disorders of amino acid metabolism might play an important role in predisposing young men to developing hypertension. The combination of metabolomics and network methods would provide another perspective on expounding the molecular mechanism underlying complex diseases.     

An in silico approach to design peptide mimetics based on docking and molecular dynamics simulation of EGFR–matuzumab complex

Epidermal growth factor receptor (EGFR) plays an essential role in anticancer therapy. Matuzumab is an antibody for the treatment of colorectal, lung and stomach cancer. Matuzumab binds efficiently to EGFR and blocks its phosphorylation. The recent clinical successes have established application of peptides for cancer treatment. The present contribution introduces an in silico approach to design peptides based on molecular dynamics simulation (MDs) of the matuzumab-EGFR complex in water environment. Moreover, principal component analysis has been used to select multiple conformations of the complex in MDs for designing the peptides. The paratope and epitope in each conformation of the complex were determined, and the alanine scanning was used to identify the hot spots of EGFR conformers. The conformations of the peptides were optimized using PEP-FOLD server and MDs. The selected conformations were analyzed in a docking study to realize the binding site of the EGFR. Finally, pharmokinetics properties of the peptides were calculated. The designed oligopeptides were EWRSYYYWH, YYYWHNEWN, YYYWHNEWS and HNHSRNYGS with a higher affinity to the EGFR relative to the previously reported peptides. The newly designed peptides were investigated for their in vivo toxicities on rats, and all of them were non-toxic.     

Analytic gradient for second order Møller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method

A new energy expression is proposed for the fragment molecular orbital method interfaced with the polarizable continuum model (FMO/PCM). The solvation free energy is shown to be more accurate on a set of representative polypeptides with neutral and charged residues, in comparison to the original formulation at the same level of the many-body expansion of the electrostatic potential determining the apparent surface charges. The analytic first derivative of the energy with respect to nuclear coordinates is formulated at the second-order M?ller-Plesset (MP2) perturbation theory level combined with PCM, for which we derived coupled perturbed Hartree-Fock equations. The accuracy of the analytic gradient is demonstrated on test calculations in comparison to numeric gradient. Geometry optimization of the small Trp-cage protein (PDB: 1L2Y) is performed with FMO/PCM/6-31(+)G(d) at the MP2 and restricted Hartree-Fock with empirical dispersion (RHF/D). The root mean square deviations between the FMO optimized and NMR experimental structure are found to be 0.414 and 0.426 A? for RHF/D and MP2, respectively. The details of the hydrogen bond network in the Trp-cage protein are revealed.     

Design and simulation of neutron radiography system based on 241Am–Be source

Neutron imaging is extended rapidly as a means of non-destructive testing (NDT) of materials. Various effective parameters on the image quality are needed to be studied for neutron radiography system with good resolution. In the present study a portable system of neutron radiography has been designed using ²⁴¹Am–Be neutron source. The effective collimator parameters were calculated to obtain relatively pure, collimated and uniform neutron beam. All simulations were carried out in two stages using MCNPX Monte Carlo code. In the first stage, different collimator configurations were investigated and the appropriate design was selected based on maximum intensity and uniformity of neutron flux at the image plane in the outlet of collimator. Then, the overall system including source, collimator and sample was simulated for achieving radiographic images of standard samples. Normalized thermal neutron fluence of 2.61×10^?5 cm^?2 per source particle with n/γ ratio of 1.92×10⁵ cm^?2 μSv^?1 could be obtained at beam port of the designed collimator. Quality of images was assessed for two standard samples, using radiographic imaging capability in MCNPX. The collimated neutron beam in the designed system could be useful in a transportable exposure module for neutron radiography application.     

Experimental data of isobaric vapour–liquid equilibrium for binary mixtures containing tetrahydrofuran and isomeric chlorobutanes

Isobaric vapour–liquid equilibrium (VLE) measurements for mixtures formed by tetrahydrofuran and isomeric chlorobutanes at 40.0?kPa (except for the mixture containing 2-methyl-2-chloropropane) and 101.3?kPa are reported. The activity coefficients were calculated from experimental data. The mixture containing 2-chlorobutane at 40.0?kPa presents an azeotrope. The VLE measurements have been found thermodynamically consistent according to Van Ness test. Wilson, NRTL, and UNIQUAC equations have been used to correlate the activity coefficients and we have obtained satisfactory results.     

Comparison of different mixing rules for prediction of density and residual internal energy of binary and ternary Lennard–Jones mixtures

Mixing rules are necessary when equations of state for pure fluids are used to calculate various thermodynamic properties of fluid mixtures. The well-known van der Waals one-fluid (vdW1) mixing rules are proved to be good ones and widely used in different equations of state. But vdW1 mixing rules are valid only when molecular size differences of components in a mixture are not very large. The vdW1 type density-dependent mixing rule proposed by Chen et al. [1] is superior for the prediction of pressure and vapor–liquid equilibria when components in the mixture have very different sizes. The extension of the mixing rule to chain-like molecules and heterosegment molecules was also made with good results. In this paper, the comparison of different mixing rules are carried out further for the prediction of the density and the residual internal energy for binary and ternary Lennard–Jones (LJ) mixtures with different molecular sizes and different molecular interaction energy parameters. The results show that the significant improvement for the prediction of densities is achieved with the new mixing rule [1], and that the modification of the mixing rule for the interaction energy parameter is also necessary for better prediction of the residual internal energy.     

A novel colorimetric aptasensor for detection of chloramphenicol based on lanthanum ion–assisted gold nanoparticle aggregation and smartphone imaging

A label-free, rapid response colorimetric aptasensor for sensitive detection of chloramphenicol (CAP) was proposed, which was based on the strategy of ssDNA-modified gold nanoparticle (AuNP) aggregation assisted by lanthanum (La³⁺) ions. The AuNPs generated a color change that could be monitored in the red, green, and blue and analyzed by the smartphone imaging app. La³⁺, as a trigger agent, strongly combined with the phosphate groups of the surface of ssDNA-AuNPs probe, which helps create AuNP aggregation and the color change of AuNPs from red to blue. On the contrary, when mixing with CAP, the aptamer (Apt) bound to CAP to form a rigid structure of the Apt-CAP complex, and La³⁺ attached to the phosphate groups of the complex, which prevented the aptamer from binding to the surface of the AuNPs. As a result, the color of the AuNPs changed to violet-red. Finally, UV-vis absorption spectroscopy and the smartphone imaging app were employed to determine CAP with a lower detection limit of 7.65 nM and 5.88 nM, respectively. The proposed strategy featuring high selectivity and strong anti-interference ability for detection of CAP in practical samples was achieved. It is worth mentioning that the simple and portable colorimetric aptasensor will be used for facilitating on-site detection of food samples.

     

A new equation for the correlation of surface tension–composition data of solvent–solvent and solvent–fused salt mixtures

An attempt has been made to propose accurate equations for correlating the surface tension of binary liquid mixtures. The method is applicable to the systems comprising of components with widely different molecular sizes. Two adjustable parameters, δ_p and δ_m obtained from the least squares analyses of the surface tension–composition data are reported for a number of systems. Temperature dependence of δ_p and δ_m is demonstrated for a few systems. The framework of operational equations has later been applied to cover multi-component systems comprising of fused salts with a single liquid component in full mole fraction range. Excellent fits of the surface tension for binary, ternary and multi-component ionic systems in aqueous or non-aqueous media have been obtained from the proposed method. The surface tension–composition data of 59 different types of systems with about 400 data points can be correlated by the equation with an average percent deviation of about 0.61. In contrast to previous equations from literature to calculate surface tension data, the proposed correlation is noted to be more accurate in different situations.     

Comparison of three enthalpy relaxation models based on fictive temperature and nonlinear Adam–Gibbs formulation

Journal of Thermal Analysis and Calorimetry - The phenomenological models based on fictive temperature and nonlinear Adam–Gibbs formulation have been widely used to describe the enthalpy...     

Molecular structure determination of solid carbon dioxide phase IV at high pressures and temperatures based on Møller-Plesset perturbation theory

Carbon dioxide has attracted considerable attention owing to its physics and abundant polymorphs. Despite decades of extensive experiments and theoretical simulations, the structure and properties of carbon dioxide under extreme pressures and temperatures are yet to be properly understood. Particularly, the intermediate phase IV of solid carbon dioxide, which separates the molecular phases at low pressures from the non-molecular phases at high pressures, has not been fully investigated, and its structure remains controversial. Here, based on the second-order Møller-Plesset perturbation (MP2) theory and the embedded fragment method, we study the crystal structure, equation of state, and Raman spectra of solid carbon dioxide phase IV at high pressures and temperatures. We demonstrate that the solid carbon dioxide phase IV is a molecular structure that remains in a molecular state rather than the bent state shown in other literature works, which is consistent with the experimental work by Datchi et al and denies the observed results by Park et al. The proposed work is of great significance in determining the structure of the high-pressure phases of carbon dioxide and further exploring the new phase of molecular crystals.     

Direct infusion electrospray ionization–ion mobility–mass spectrometry for comparative profiling of fatty acids based on stable isotope labeling

A rapid method for fatty acids (FAs) comparative profiling based on carboxyl-specific stable isotope labeling (SIL) and direct infusion electrospray ionization–ion mobility–mass spectrometry (ESI–IM–MS) is established. The design of the method takes advantage of the three-dimensional characteristics of IM–MS including drift time, m/z and ion intensity, for comparison of d0-/d6-2,4-dimethoxy-6-piperazin-1-yl pyrimidine (DMPP)-labeled FAs. In particular, without chromatographic separation, the method allowed direct FAs profiling in complex samples due to the advantageous priority of DMPP in signal enhancement as well as the extra resolution that IM–MS offered. Additionally, the d0-/d6-DMPP-labeled FAs showed expected features, including very similar drift times, 6 Da mass deviations, specific reporter ions, similar MS responses, and adherence to the drift time rule regarding the influence of carbon chain length and unsaturation on relative drift times. Therefore, the introduction of isotope analogs minimized the matrix effect and variations in quantification and ensured accurate identification of non-targeted FAs by those typical features. Peak intensity ratios between d0-/d6-DMPP-labeled ions were subsequently used in relative quantification for the detected FAs. The established strategy has been applied successfully in the rapid profiling of trace free FAs between normal and cancerous human thyroid tissues. Sixteen free FAs were found with the increased level with a statistically significant difference (p < 0.05) compared to the normal tissue samples. The integrated SIL technique and ESI–IM–MS are expected to serve as an alternative tool for high-throughput analysis of FAs in complex samples.     

Analysis of pseudo jahn–teller distortion based on natural bond orbital theory: Case study for silicene

Ground state (GS) instability of nondegenerate molecules in high symmetric structures is understood through Pseudo Jahn–Teller mixing of the electronic states through the vibronic coupling. The general approach involves setting up of a Pseudo Jahn–Teller (PJT) problem wherein one or more symmetry allowed excited states couple to the GS to create vibrational instability along a normal mode. This faces two major complications namely (1) estimating the adiabatic potential energy surfaces for the excited states which are often difficult to describe in case the excited states have charge-transfer or multi-excitonic (ME) character and (2) finding out how many such excited states (all satisfying the symmetry requirements for vibronic coupling) of increasing energies need to be coupled with the GS for a particular PJT problem. An analogous alternative approach presented here for the well-known case of symmetry breaking of planar (D_6h) hexasilabenzene (Si₆H₆) to the buckled (D_3d) structure involves identifying the second-order donor–acceptor, hyperconjugative interactions (E²_{i → j}) that stabilize the distorted structure. Following the recent work of Nori-Shargh and Weinhold, one observes that the orbitals involved in the vibronic coupling between the S₀/S_n states and those for the donor (filled)–acceptor (empty) interactions are identical. In fact, deletion of any particular pair of E²_{i → j} interaction creates vibrational instability in the buckled structure and as a corollary, deleting it for the planar structure removes its instability. The one-to-one correlation between the natural bond orbital theory and PJT theory assists in an intuitive identification of the relevant (few) excited states from a manifold of computed ones that cause symmetry breaking by vibronic coupling. © 2019 Wiley Periodicals, Inc.     

Molecular simulation of the phase behaviour of ternary fluid mixtures: the effect of a third component on vapour–liquid and liquid–liquid coexistence

The Gibbs ensemble algorithm is implemented to determine the vapour–liquid and liquid–liquid phase coexistence of dilute ternary fluid mixtures interacting via a Lennard–Jones potential. Calculations are reported for mixtures with a third component characterised by different intermolecular potential energy parameters. Comparison with binary mixture data indicates that the choice of energy parameter for the third component affects the composition range of vapour–liquid substantially. The addition of a third component lowers the energy of liquid phase while slightly increasing the energy of the vapour phase.     

Investigation of π–π and ion–dipole interactions on 1-allyl-3-butylimidazolium ionic liquid-modified silica stationary phase in reversed-phase liquid chromatography

1-Allyl-3-butylimidazolium bromide ionic liquid [AyBIm]Br was prepared and used for the modification of mercaptopropyl-functionalized silica through surface radical chain-transfer addition. The obtained ionic liquid-modified silica (SiImBr) was characterized by elemental analysis, infrared spectroscopy, NMR spectroscopy, and thermogravimetric analysis. The selective retention behaviours of polycyclic aromatic hydrocarbons (PAHs) including some positional isomers were investigated using SiImBr as a stationary phase in reversed-phase liquid chromatography. The results showed that SiImBr presented multiple interactions including hydrophobic, π–π, and ion–dipole interactions during the separation of PAHs and dipolar compounds. However, it is proposed that π–π and ion–dipole interactions play important roles in the separation of PAHs and dipolar compounds. These results indicate that the ionic liquid-modified silica stationary phase is promising for future applications. A commercially available monomeric octadecylated silica (ODS) column and a custom-made poly(styrene)-grafted silica (Sil-St_n) column were used as references.