Density functional theory model of adsorption on amorphous and microporous silica materials

We present a novel quenched solid density functional theory (QSDFT) model of adsorption on heterogeneous surfaces and porous solids, which accounts for the effects of surface roughness and microporosity. Within QSDFT, solid atoms are considered as quenched component(s) of the solid-fluid system with given density distribution(s). Solid-fluid intermolecular interactions are split into hard-sphere repulsive and mean-field attractive parts. The former are treated with the multicomponent fundamental measure density functional. Capabilities of QSDFT are demonstrated by drawing on the example of adsorption on amorphous silica materials. We show that, using established intermolecular potentials and a realistic model for silica surfaces, QSDFT quantitatively describes adsorption/desorption isotherms of Ar and Kr on reference MCM-41, SBA-15, and LiChrosphere materials in a wide range of relative pressures. QSDFT offers a systematic approach to the practical problems of characterization of microporous, mesoporous, and amorphous silica materials, including an assessment of microporosity, surface roughness, and adsorption deformation. Predictions for the pore diameter and the extent of pore surface roughness in MCM-41 and SBA-15 materials are in very good agreement with recent X-ray diffraction studies.     

Characterization of the pore structure of three-dimensionally ordered mesoporous carbons using high resolution gas sorption

The use of colloidal crystals with various primary particle sizes as templates leads to the formation of three-dimensionally ordered mesoporous (3DOm) carbons containing spherical pores with tailorable pore size and extremely high pore volumes. We present a comprehensive structural characterization of these novel carbons by using nitrogen (77.4 K) and argon (87.3 K) adsorption coupled with the application of novel, dedicated quenched solid density functional theory (QSDFT) methods which assume correctly the underlying spherical pore geometry and also the underlying adsorption mechanism. The observed adsorption isotherms are of Type IV with Type H1-like hysteresis, despite the fact that pore blocking affects the position of the desorption branch. This follows also from detailed, advanced scanning hysteresis experiments which not only allow one to identify the underlying mechanisms of hysteresis, but also provide complementary information about the texture of these unique porous materials. This work addresses the problem of pore size analysis of novel, ordered porous carbons and highlights the importance of hysteresis scanning experiments for textural analysis of the pore network.     

Assessing surface chemistry and pore structure of active carbons by a combination of physisorption (H2O, Ar, N2, CO2), XPS and TPD-MS

In order to address open questions concerning the surface chemistry and pore structure characterization of nanoporous carbons, we performed extensive experiments by combining various experimental techniques on a series of commercially available activated carbons which exhibit diverse surface chemistry characteristics. Pore size analysis was performed on Ar (87 K), N₂ (77 K) and CO₂ (273 K) adsorption isotherms using state-of-the art methods based on density functional theory, including the recently developed quenched solid density functional theory (QSDFT). A detailed study of the surface chemistry was obtained by applying temperature programmed desorption coupled with mass spectrometry (TPD-MS) as well as XPS (X-Ray-Photoelectron Scattering). This information together with the pore structure information leads to a reliable interpretation of systematic water adsorption measurements obtained on these materials. Our results clearly suggest that water adsorption is indeed a sensitive tool for detecting differences in surface chemistry between chemically and physically activated active carbon materials with comparable ultramicropore structure. The occurrence of sorption hysteresis associated with the filling of micro- and narrow mesopores (in a range where nitrogen and argon isotherms are reversible) provides additional structural information, complementary to the insights from argon/nitrogen/carbon dioxide adsorption.     

Solvation forces between molecularly rough surfaces

Surface heterogeneity affects significantly wetting and adhesion properties. However, most of the theories and simulation methods of calculating solid-fluid interactions assume a standard thermodynamic model of the Gibbs' dividing solid-fluid interface, which is molecularly smooth. This assumption gives rise to a layering of the fluid phase near the surface that is displayed in oscillating density profiles in any theories and simulation models, which account for the hard core intermolecular repulsion. This layering brings about oscillations of the solvation (or disjoining) pressure as a function of the gap distance, which are rarely observed in experiments, except for ideal monocrystal surfaces. We present a detailed study of the effects of surface roughness on the solvation pressure of Lennard-Jones (LJ) fluids confined by LJ walls based on the quenched solid density functional theory (QSDFT). In QSDFT, the surface roughness is quantified by the roughness parameter, which represents the thickness of the surface "corona" - the region of varying solid density. We show that the surface roughness of the amplitude comparable with the fluid molecular diameter effectively damps the oscillations of solvation pressure that would be observed for molecularly smooth surfaces. The calculations were done for the LJ model of nitrogen sorption at 74.4 K in slit-shaped carbon nanopores to provide an opportunity of comparing with standard adsorption experiments. In addition to a better understanding of the fundamentals of fluid adsorption on heterogeneous surfaces and inter-particle interactions, an important practical outcome is envisioned in modeling of adsorption-induced deformation of compliant porous substrates.     

微介孔材料的孔结构分析表征

孔材料的研究是当今热点问题之一，而关于孔的结构特性如比表面积、孔容、孔尺寸及分布等相关参数的确定，对于一些研究者可能存在着认知盲区.以实验室自制的孔材料为例，应用Nova 1000e型比表面积测试仪进行相关测试，并采用不同方法获得材料的孔结构参数.试验结果表明，非定域密度泛函理论（NLDFT）和骤冷固体密度泛函理论（QSDFT）可获取较为全面的材料孔结构参数，分析过程简便快捷.     

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations

A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages. In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged elastic band methods, which are powerful techniques for studying reaction pathways in a highly parallel (i.e., parallel/parallel) fashion, with each pathway point being distributed to a different node of a large cluster. To test our implementation, a series of systems were studied and comparisons were made to both full QM calculations and previous QM/MM studies and experiments. For instance, the differences between HF, DFT, MP2, and CCSD QM/MM calculations of H2O...H2O, H2O...Na+, and H2O...Cl- complexes have been explored. Furthermore, the recently implemented polarizable Drude water model was used to make comparisons to the popular TIP3P and TIP4P water models for doing QM/MM calculations. We have also computed the energetic profile of the chorismate mutase catalyzed Claisen rearrangement at various QM/MM levels of theory and have compared the results with previous studies. Our best estimate for the activation energy is 8.20 kcal/mol and for the reaction energy is -23.1 kcal/mol, both calculated at the MP2/6-31+G(d)//MP2/6-31+G(d)/C22 level of theory.     

Comparative study of generalized born models: Born radii and peptide folding

In this study, we have implemented four analytical generalized Born (GB) models and investigated their performance in conjunction with the GROMOS96 force field. The four models include that of Still and co-workers, the HCT model of Cramer, Truhlar, and co-workers, a modified form of the AGB model of Levy and co-workers, and the GBMV2 model of Brooks and co-workers. The models were coded independently and implemented in the GROMOS software package and in TINKER. They were compared in terms of their ability to reproduce the results of Poisson-Boltzmann (PB) calculations and in their performance in the ab initio peptide folding of two peptides, one that forms a beta-hairpin in solution and one that forms an alpha-helix. In agreement with previous work, the GBMV2 model is most successful in reproducing PB results while the other models tend to underestimate the effective Born radii of buried atoms. In contrast, stochastic dynamics simulations on the folding of the two peptides, the C-terminus beta-hairpin of the B1 domain of protein G and the alanine-based alpha-helical peptide 3K(I), suggest that the simpler GB models are more effective in sampling conformational space. Indeed, the Still model used in conjunction with the GROMOS96 force field is able to fold the hairpin peptide to a native-like structure without the benefit of enhanced sampling techniques. This is due in part to the properties of the united-atom GROMOS96 force field which appears to be more flexible, and hence to sample more efficiently, than force fields such as OPLSAA. Our results suggest a general strategy which involves using different combinations of force fields and solvent models in different applications, for example, using GROMOS96 and a simple GB model in sampling and OPLSAA and a more accurate GB model in refinement. The fact that various methods have been implemented in a unified way should facilitate the testing and subsequent use of different methods to evaluate conformational free energies in different applications. Our results also bear on some general issues involved in peptide folding and structure prediction which are addressed in the Discussion.     

Pharmacophore modeling and in silico screening for new P450 19 (aromatase) inhibitors

Cytochrome P450 19 (P450 19, aromatase) constitutes a successful target for the treatment of breast cancer. This study analyzes chemical features common to P450 19 inhibitors to develop ligand-based, selective pharmacophore models for this enzyme. The HipHop and HypoRefine algorithms implemented in the Catalyst software package were employed to create both common feature and quantitative models. The common feature model for P450 19 includes two ring aromatic features in its core and two hydrogen bond acceptors at the ends. The models were used as database search queries to identify active compounds from the NCI database.     

Carbon slit pore model incorporating surface energetical heterogeneity and geometrical corrugation

In our recent paper (Jagiello and Olivier, Carbon 55:70–80, 2013) we considered introducing energetical heterogeneity (EH) and geometrical corrugation (GC) to the pore walls of the standard carbon slit pore model. We treated these two effects independently and we found that each of them provides significant improvement to the carbon model. The present work is a continuation of the previous one, as we include both effects in one comprehensive model. The existing standard slit pore model widely used for the characterization of activated carbons assumes graphite-like energetically uniform pore walls. As a result of this assumption adsorption isotherms calculated by the non-local density functional theory (NLDFT) do not fit accurately the experimental N₂ data measured for real activated carbons. Assuming a graphene-based structure for activated carbons and using a two-dimensional-NLDFT treatment of the fluid density in the pores we present energetically heterogeneous and geometrically corrugated (EH–GC) surface model for carbon pores. Some parameters of the model were obtained by fitting the model to the reference adsorption data for non-graphitized carbon black. For testing, we applied the new model to the pore size analysis of porous carbons that had given poor results when analyzed using the standard slit pore model. We obtained an excellent fit of the new model to the experimental data and we found that the typical artifacts of the standard model were eliminated.     

Hybrid MPI/OpenMP parallelization of the effective fragment potential method in the libefp software library

A new hybrid MPI/OpenMP parallelization scheme is introduced for the Effective Fragment Potential (EFP) method implemented in the libefp software library. The new implementation employs dynamic load balancing algorithm that uses a master/slave model. The software shows excellent parallel scaling up to several hundreds of CPU‐cores across multiple nodes. The code uses functions only from the well‐established MPI‐1 standard that simplifies portability of the library. This new parallel EFP implementation greatly expands the applicability of the EFP and QM/EFP methods by extending attainable time‐ and length‐scales. © 2014 Wiley Periodicals, Inc.     

随机孔模型应用于煤焦与CO2气化的动力学研究

考察970 ℃～1 165 ℃，北宿、神府、忻州、潞安煤焦与CO2在热天平中的气化反应，用恒温法进行热重分析，考察煤种、气化温度、灰分对煤焦气化的影响。用随机孔模型模拟北宿煤反应速率与碳转化率的关系曲线，与未反应芯缩核模型和混合模型模拟结果比较。在化学控制区内，实验数据用随机孔模型拟合最佳。1 066 ℃和1 165 ℃气化数据拟合的相关系数为0.99，970 ℃拟合效果较差。随机孔模型作为简单、精度高的模型可应用于煤炭气化反应中。应用此模型计算四种煤焦反应活化能、指前因子、孔结构参数、A0等动力学参数值。同一煤种气化反应温度越高初始反应速率越大，结构参数体现了孔结构变化对反应的影响，随着温度的升高值减小。     

Immersion Calorimetry: Molecular Packing Effects in Micropores

Repeated and controlled immersion calorimetry experiments were performed to determine the specific surface area and pore‐size distribution (PSD) of a well‐characterized, microporous poly(furfuryl alcohol)‐based activated carbon. The PSD derived from nitrogen gas adsorption indicated a narrow distribution centered at 0.57±0.05 nm. Immersion into liquids of increasing molecular sizes ranging from 0.33 nm (dichloromethane) to 0.70 nm (α‐pinene) showed a decreasing enthalpy of immersion at a critical probe size (0.43–0.48 nm), followed by an increase at 0.48–0.56 nm, and a second decrease at 0.56–0.60 nm. This maximum has not been reported previously. After consideration of possible reasons for this new observation, it is concluded that the effect arises from molecular packing inside the micropores, interpreted in terms of 2D packing. The immersion enthalpy PSD was consistent with that from quenched solid density functional theory (QSDFT) analysis of the nitrogen adsorption isotherm.     

Tailoring pore size and pore size distribution of kidney dialysis hollow fiber membranes via dual-bath coagulation approach

Polyethersulfone (PES) hollow fiber membranes for kidney dialysis application were prepared by the dry-jet wet-spinning method. A dual-coagulation bath technology was first time employed for fabricating the kidney dialysis membranes with a tight inner skin and loose outer supporting layer structure. A weak coagulant isopropanol (IPA) was served as the first external coagulation bath, while water as the second bath. Experiments demonstrate their advantages of better controlling both inner and outer skin morphology. The as-spun fibers have a higher mean effective pore size (μ_p), pure water permeation flux (PWP) and molecular weight cut-off (MWCO) with an increase in N-methyl-2-pyrrolidone (NMP) percentage in bore fluid (i.e., internal coagulant). After being treated in 8000 ppm NaOCl solution for 1 day, fibers show larger pore sizes and porosity in both inner and outer surfaces, and thinner inner and outer layers than their as-spun counterparts. Among them, the bleached fibers spun with 50 wt.% NMP in bore fluid have the MWCO (43 kDa) and PWP (40 × 10⁻⁵ L m⁻² Pa⁻¹ h⁻¹) suitable for kidney dialysis application. Based on SEM observations and solute rejection performance, the further heat treated fibers in an aqueous solution is found to be an effective way to fine tune membranes morphology and MWCO for kidney dialysis application. The solute rejection performance data of the hollow fiber membranes spun with 55 wt.% NMP in bore fluid after heat treated at 90 °C in water for 2 h were found to be very appropriate for the kidney dialysis application.     

Influence of the pore structure of MCM-41 and SBA-15 silica fibers on atomic layer chemical vapor deposition of cobalt carbonyl

Mesoporous high surface area MCM-41 and SBA-15 type silica materials with fibrous morphology were synthesized and used as support materials for the ALCVD (atomic layer chemical vapor deposition) preparation of Co/MCM-41 and Co/SBA-15 catalysts. Co/MCM-41 and Co/SBA-15 catalysts were prepared by deposition of Co2(CO)8 from the gas phase onto the surfaces of preheated support materials in a fluidized bed reactor. For both silica materials, two different kinds of preparation methods, direct deposition and a pulse deposition method, were used. Pure silica supports as well as supported cobalt catalysts were characterized by various spectroscopic (IR) and analytical (X-ray diffraction, Brunauer-Emmett-Teller, elemental analysis) methods. MCM-41 and SBA-15 fibers showed considerable ability to adsorb Co2(CO)8 from the gas phase. For MCM-41 and SBA-15 silicas, cobalt loadings of 13.7 and 12.1 wt % were obtained using the direct deposition method. The cobalt loadings increased to 23.0 and 20.7 wt % for MCM-41 and SBA-15 silicas, respectively, when the pulse deposition method was used. The reduction behavior of silica-supported cobalt catalysts was found to depend on the catalyst preparation method and on the mesoporous structure of the support material. Almost identical reduction properties of SBA-15-supported catalysts prepared by different deposition methods are explained by the structural properties of the mesoporous support and, in particular, by the chemical structure of the inner surfaces and walls of the mesopores. Pulse O2/H2 chemisorption experiments showed catalytically promising redox properties and surface stability of the prepared MCM-41- and SBA-15-supported cobalt catalysts.     

Parallel pore and surface diffusion of levulinic acid in basic polymeric adsorbents

The equilibrium and kinetics of levulinic acid (LA) adsorption on two basic polymeric adsorbents, 335 (highly porous gel) and D315 (macroreticular), were investigated. Experimental adsorption rates in batch stirred vessels under a variety of operating conditions were described successfully by the parallel pore and surface diffusion model taking into account external mass transfer and nonlinear Toth isotherm. The film-pore diffusion model was matched with the rate data and the resulting apparent pore diffusivities were strongly concentration-dependent and approached to a constant value for 335 adsorbent. Thus, the constant value was taken as the accurate pore diffusivity, while the pore diffusivity in D315 was estimated from the particle porosity. The surface diffusivities decreased with increasing initial bulk concentration for both adsorbents. The inverse concentration dependence was correlated reasonably well to the change of isosteric heat of adsorption as amount adsorbed.     

An extensible interface for QM/MM molecular dynamics simulations with AMBER

We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface. © 2013 Wiley Periodicals, Inc.     

Effect of the pore geometry in the characterization of the pore size distribution of activated carbons

In this work, the characterization of Activated Carbons (AC) by using the independent pore models is discussed, with special emphasis on the issue of how the assumed pore geometry can affect the resulting Pore Size Distribution (rPSD) and on the problem of the unicity of the PSD when different probe molecules are used in adsorption experiments. A theoretical test was performed using virtual solids based in the so-called Mixed Geometry Model (MGM) (Azevedo et al. 2010). The MGM uses a kernel of adsorption isotherms generated by GCMC for different pore sizes and two pore geometries: slit and triangular. The adsorption isotherms of a virtual MGM solid were fitted with both the traditional Slit Geometry Model (SGM) and the Mixed Geometry Model (MGM). It is demonstrated that, by assuming a different pore geometry model from that of the real sample, different PSDs may be obtained by fitting adsorption isotherms of different probe gases. Finally, experimental results are shown which both point toward the MGM as an acceptable extension of the SGM and confirm that the MGM is a closer representation of the actual porous structure of most activated carbons.     

Microstructural model for prediction of stress–strain curves of amorphous and semicrystalline elastomers

A fundamental microstructural model was developed to calculate the stress–strain curves of rubbery amorphous polymers and of semicrystalline polymers with a rubbery amorphous phase by numerical simulations. The rubbery amorphous phase was treated by using a version of the theory of rubber elasticity with finite extensibility. Physical entanglements and chemical crosslinks were both allowed. Slippage was implemented by a Monte Carlo algorithm controlled by kinetic parameters such as the activation energy and activation volume for slippage. The crystalline phase was treated in a very idealized manner, including a crude representation of tie chains but not taking the internal structure of the crystallites into account. A two-dimensional embodiment of the model was implemented into software. For amorphous polymers, while lacking truly quantitative accuracy, the model showed sufficiently good agreement with the experimental trends to be used as a qualitative or semiquantitative predictive tool, and it is currently being used in this manner. The more complex semicrystalline version was less accurate and will need to be improved in future work. Most of the limitations of the semicrystalline version could be ascribed unambiguously to specific simplifications made in the software implementation to reduce the amount of computer time required for the calculations. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 2715–2739, 1997     

Excited-State Electronic Structure with Configuration Interaction Singles and Tamm-Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units

Excited-state calculations are implemented in a development version of the GPU-based TeraChem software package using the configuration interaction singles (CIS) and adiabatic linear response Tamm-Dancoff time-dependent density functional theory (TDA-TDDFT) methods. The speedup of the CIS and TDDFT methods using GPU-based electron repulsion integrals and density functional quadrature integration allows full ab initio excited-state calculations on molecules of unprecedented size. CIS/6-31G and TD-BLYP/6-31G benchmark timings are presented for a range of systems, including four generations of oligothiophene dendrimers, photoactive yellow protein (PYP), and the PYP chromophore solvated with 900 quantum mechanical water molecules. The effects of double and single precision integration are discussed, and mixed precision GPU integration is shown to give extremely good numerical accuracy for both CIS and TDDFT excitation energies (excitation energies within 0.0005 eV of extended double precision CPU results).     

A general variance model in methods comparison

Valid statistical tests of paired data require correct models of how measurement variance depends on analyte concentration. One often‐used assumption is that the variance is constant across the range; another is that the coefficient of variation is constant. But in many data sets, neither of these holds. A variance model containing both a constant variance and a constant coefficient of variation term is recommended as an often‐useful additional analysis tool for methods comparison. The more general variance model is fitted to a simulated data set, and one from a clinical chemistry methods comparison. It is used to provide more reliable average versus difference plots, to fit weighted Deming regressions, and to provide valid paired data analyses. The calculations are implemented in r software. Copyright © 2013 John Wiley & Sons, Ltd.