Using quaternions to calculate RMSD

Coutsias, Evangelos A.,Seok, Chaok,Dill, Ken A. John Wiley Sons, Inc. 2004 Journal of computational chemistry Vol.25 No.15

<P>A widely used way to compare the structures of biomolecules or solid bodies is to translate and rotate one structure with respect to the other to minimize the root-mean-square deviation (RMSD). We present a simple derivation, based on quaternions, for the optimal solid body transformation (rotation-translation) that minimizes the RMSD between two sets of vectors. We prove that the quaternion method is equivalent to the well-known formula due to Kabsch. We analyze the various cases that may arise, and give a complete enumeration of the special cases in terms of the arrangement of the eigenvalues of a traceless, 4 × 4 symmetric matrix. A key result here is an expression for the gradient of the RMSD as a function of model parameters. This can be useful, for example, in finding the minimum energy path of a reaction using the elastic band methods or in optimizing model parameters to best fit a target structure. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1849–1857, 2004</P> <B>Graphic Abstract</B> <img src='wiley_img/01928651-2004-25-15-JCC20110-gra001.gif' alt='wiley_img/01928651-2004-25-15-JCC20110-gra001'>

An efficient molecular docking using conformational space annealing

Lee, Kyoungrim,Czaplewski, Cezary,Kim, Seung-Yeon,Lee, Jooyoung John Wiley Sons, Inc. 2005 Journal of computational chemistry Vol.26 No.1

<P>Molecular docking falls into the general category of global optimization problems because its main purpose is to find the most stable complex consisting of a receptor and its ligand. Conformational space annealing (CSA), a powerful global optimization method, is incorporated with the Tinker molecular modeling package to perform molecular docking simulations of six receptor–ligand complexes (3PTB, 1ULB, 2CPP, 1STP, 3CPA, and 1PPH) from the Protein Data Bank. In parallel, Monte Carlo with the minimization (MCM) method is also incorporated into the Tinker package for comparison. The energy function, consisting of electrostatic interactions, van der Waals interactions, and torsional energy terms, is calculated using the AMBER94 all-atom empirical force field. Rigid docking simulations for all six complexes and flexible docking simulations for three complexes (1STP, 3CPA, and 1PPH) are carried out using the CSA and the MCM methods. The simulation results show that the docking procedures using the CSA method generally find the most stable complexes as well as the native-like complexes more efficiently and accurately than those using the MCM, demonstrating that CSA is a promising search method for molecular docking problems. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 78–87, 2005</P> <B>Graphic Abstract</B> <img src='wiley_img/01928651-2005-26-1-JCC20147-gra001.gif' alt='wiley_img/01928651-2005-26-1-JCC20147-gra001'>

Accelerated long‐range corrected exchange functional using a two‐gaussian operator combined with one‐parameter progressive correlation functional [LC‐BOP(2Gau)]

Song, Jong‐,Won,Hirao, Kimihiko John Wiley Sons, Inc. 2019 Journal of computational chemistry Vol.40 No.1

<P>Recently, we proposed a simple yet efficient method for the computation of a long‐range corrected (LC) hybrid scheme [LC‐DFT(2Gau)], which uses a modified two‐Gaussian attenuating operator instead of the error function for the long‐range HF exchange integral. This method dramatically reduced the computational time while maintaining the improved features of the LC density functional theory (DFT). Here, we combined an LC hybrid scheme using a two‐Gaussian attenuating operator with one‐parameter progressive correlation functional and Becke88 exchange functional with varying range‐separation parameter values [LC‐BOP(2Gau) with various <I>μ</I> values of 0.16, 0.2, 0.25, 0.3, 0.35, 0.4, and 0.42] and demonstrated that LC‐BOP(2Gau) reproduces well the thermochemical and frontier orbital energies of LC‐BOP. Additionally, we revised the scaling factors of the Gaussian multipole screening scheme for LC‐DFT(2Gau) to correspond to the angular momentum of orbitals, which decreased the energy deviations from the energy with the no‐screening scheme. © 2018 Wiley Periodicals, Inc.</P>

Preparation of a monolithic and macroporous superabsorbent polymer via a high internal phase Pickering emulsion template

Shin, Heewoong,Kim, Subeen,Han, YoungKyu,Kim, KyuHan,Choi, Siyoung Q. John Wiley Sons, Inc. 2019 Journal of applied polymer science Vol.136 No.42

<P><B>ABSTRACT</B></P><P>A superabsorbent polymer (SAP) possesses an ability to absorb an aqueous solution up to several hundred times its own weight. To utilize a SAP effectively, a high absorption rate is also essential in addition to a high absorption capability. Herein, using a template based on a high internal phase Pickering emulsion (HIPPE) stabilized by aluminum oxide (Al<SUB>2</SUB>O<SUB>3</SUB>) nanoparticles, we synthesize a SAP with a high absorption rate by forming macropores. In particular, by adjusting three different parameters, the concentration of the crosslinker, the internal volume fraction of the emulsion, and the particle concentration, we successfully formed a HIPPE‐templated SAP with a high absorption rate for a saline solution, which was 51.6 g g<SUP>−1</SUP> of the absorbency within 10 s. We confirm that the swelling kinetics is mainly determined by the interconnectivity between the internal macro‐pores. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. <B>2019</B>, <I>136</I>, 48133.</P>

Optical properties of poly(vinyl chloride)‐gel‐based microlens arrays

Zhou, Zuowei,Ren, Hongwen John Wiley Sons, Inc. 2019 Journal of applied polymer science Vol.136 No.10

<P><B>ABSTRACT</B></P><P>We use a poly(vinyl chloride) (PVC) gel and an electrode to fabricate adaptive microlens arrays (MLAs). The electrode has a zoned‐array pattern. By applying a direct current voltage to the electrode, the PVC gel on each zoned electrode exhibited the character of a lens. The imaging of the MLA can be analyzed using either an optical microscope or a beam profiler or both. The topography of the PVC gel can be measured using an optical surface profiler. Compared to the imaging and focusing, the topographic map can discover additional information about the performances of the MLA. For example, the focal length of each lens in the MLA can be calculated precisely, and the aberration of the MLA can also be evaluated. Results show that the surface profile is an important factor for characterizing the performance of PVC‐gel‐based MLA. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. <B>2019</B>, <I>136</I>, 47407.</P>

Sustainable rigid polyurethane foams based on recycled polyols from chemical recycling of waste polyurethane foams

Shin, Se‐,Ra,Kim, Han‐,Na,Liang, Jing‐,Yu,Lee, Sang‐,Hyub,Lee, Dai‐,Soo John Wiley Sons, Inc. 2019 Journal of applied polymer science Vol.136 No.35

<P><B>ABSTRACT</B></P><P>The preparation and characteristics of rigid polyurethane foams (RPUFs) based on recycled polyol obtained by glycolysis of waste RPUF scraps from end‐of‐life refrigerators were investigated. To deactivate the amine adducts derived from isocyanates, the recycled product obtained after depolymerization was chemically modified via addition polymerization of propylene oxide. Two kinds of recycled polyols with different hydroxyl values and viscosity were blended with conventional virgin polyether polyol to prepare the RPUFs. The effects of the recycled polyols on the physical properties of RPUFs such as cell structures, compressive strength, thermal conductivity, and limiting oxygen index were discussed. It was found that the RPUFs from recycled polyols showed superior compressive strength, thermal insulation property, and self‐extinguishing property compared with conventional control foam. The results of this study reveal that the recycled polyols could be used as feedstock for RPUFs with superior performance. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. <B>2019</B>, <I>136</I>, 47916.</P>

GalaxyTongDock: Symmetric and asymmetric <i>ab initio</i> protein–protein docking web server with improved energy parameters

Park, Taeyong,Baek, Minkyung,Lee, Hasup,Seok, Chaok John Wiley Sons, Inc. 2019 Journal of computational chemistry Vol.40 No.27

<P>Protein–protein docking methods are spotlighted for their roles in providing insights into protein–protein interactions in the absence of full structural information by experiment. GalaxyTongDock is an <I>ab initio</I> protein–protein docking web server that performs rigid‐body docking just like ZDOCK but with improved energy parameters. The energy parameters were trained by iterative docking and parameter search so that more native‐like structures are selected as top rankers. GalaxyTongDock performs asymmetric docking of two different proteins (GalaxyTongDock_A) and symmetric docking of homo‐oligomeric proteins with C<SUB>n</SUB> and D<SUB>n</SUB> symmetries (GalaxyTongDock_C and GalaxyTongDock_D). Performance tests on an unbound docking benchmark set for asymmetric docking and a model docking benchmark set for symmetric docking showed that GalaxyTongDock is better or comparable to other state‐of‐the‐art methods. Experimental and/or evolutionary information on binding interfaces can be easily incorporated by using block and interface options. GalaxyTongDock web server is freely available at <url href='http://galaxy.seoklab.org/tongdock'>http://galaxy.seoklab.org/tongdock</url>. © 2019 Wiley Periodicals, Inc.</P>

Novel green composites from styrene butadiene rubber and palm oil derivatives for high performance tires

Lee, Chung Kyeong,Seo, Jin Gwan,Kim, Hyun Jun,Song, Sung Ho John Wiley Sons, Inc. 2019 Journal of applied polymer science Vol.136 No.25

<P><B>ABSTRACT</B></P><P>In rubber compounding, renewable, nontoxic, and degradable palm oil is used as a safe alternative softener or stabilizer process oil. In the tire industry, with the development of environment‐friendly “green tires,” silica has been used as a reinforcing filler for tread compounds. To make the hydrophilic silica compatible with the hydrophobic rubber matrix, the addition of amphiphilic oil is required. We, for the first time, prepared an amphiphilic palm oil derivative (PO) with hydrophobic and hydrophilic functional groups in bulk. Rubber composites prepared with the PO exhibited remarkable improvements in mechanical properties, including tensile strength, elongation, and fatigue. These improvements are attributed to the enhanced dispersion of the fillers in the rubber matrix due to the PO. Also, the mixing of PO in the rubber matrix resulted in outstanding abrasion, rebound resilience, and heat buildup properties at low loadings. We then prepared pneumatic tires with a tread composite using PO, and conducted virtual tests using a vehicle‐mounted pneumatic tire. The pneumatic tire exhibited enhanced high speed durability, dry and wet braking. The strong interfacial interactions between the silica and the rubber matrix due to the PO resulted in improved viscoelastic properties. These results show that PO is a renewable potential replacement for conventional aromatic oils in tire engineering applications. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. <B>2019</B>, <I>136</I>, 47672.</P>

Synthesis of emulsion styrene butadiene rubber by reversible addition–fragmentation chain transfer polymerization and its properties

Mun, Hyunsung,Hwang, Kiwon,Kim, Wonho John Wiley Sons, Inc. 2019 Journal of applied polymer science Vol.136 No.7

<P><B>ABSTRACT</B></P><P>Emulsion polymerization is generally used to synthesize styrene butadiene rubber (SBR), and the molecular weight of this rubber can be easily increased. However, the broad molecular weight distribution (MWD) of SBR increases energy loss and adversely affects the dynamic viscoelastic properties. To overcome this disadvantage, reversible addition–fragmentation chain transfer (RAFT) polymerization, which is a type of living polymerization, is applied to emulsion polymerization for preparing RAFT emulsion SBR (ESBR). The molecular weight and microstructure of RAFT ESBR are compared to those of commercially available ESBR 1502 by gel permeation chromatography and proton nuclear magnetic resonance spectroscopy. The aforementioned two polymers are used to prepare unfilled ESBR compounds, which are compared in terms of key physical properties (abrasion resistance, mechanical properties, and dynamic viscoelastic properties). It is confirmed that various physical properties of RAFT ESBR are improved due to its narrow MWD. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. <B>2019</B>, <I>136</I>, 47069.</P>

Fabrication of hybrid matrix/silane modified carbon fabric composites and study of their mechanical properties

M., Latif,M.N., Prabhakar,Song, Jung‐,il John Wiley Sons, Inc. 2019 Journal of applied polymer science Vol.136 No.26

<P><B>ABSTRACT</B></P><P>Carbon fiber reinforced polymer composites are an extremely strong and light fiber‐reinforced plastics that contains carbon fiber. In the present study, carbon fabrics were treated with various weight percentages of silane and were confirmed by spectral analysis (Fourier transform infrared). The treated carbon fibers were reinforced in hybrid resin (a combination of vinyl ester and epoxy at a ratio of 80:20) by using vacuum‐assisted resin transfer mold technique. The composites were tested to know their tensile strength, modulus, flexural strength, modulus, and interlaminar shear strength. The hybrid matrix specimen was also prepared and tested for the mechanical properties and confirmed the miscibility by differential scanning calorimetry and X‐ray diffraction. The mechanical properties of hybrid matrix composites (HMCs) were studied by fracture surface morphology with scanning electron microscope. The mechanical properties of the HMCs increased with silane treatment. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. <B>2019</B>, <I>136</I>, 47695.</P>