On the DFT Ground State of Crystalline Bromine and Iodine

We report on an erroneous ground state within common density functional theory (DFT) methods for the solid elements bromine and iodine. Phonon computations at the GGA level for both molecular crystals yield imaginary vibrational modes, erroneously indicating dynamic instability—that fact alone could easily pass as a computational artefact, but these imaginary modes lead to energetically more favorable and dynamically stable structures, made up of infinite monoatomic chains. In contrast, meta‐GGA and hybrid functionals yield the correct energetic order for bromine, while for iodine, most global hybrids do not improve the GGA result significantly. The qualitatively correct answer, in both cases, is given by the long‐range corrected hybrid LC‐ωPBE, the Minnesota functionals M06L and M06, and by periodic Hartree–Fock and MP2 theory. This poor performance of economic DFT functionals should be kept in mind, for example, during global structure optimizations of systems with significant contributions from halogen bonds.     

Retention time prediction of compounds in Grob standard mixture for apolar capillary columns in temperature-programmed gas chromatography

This paper presents an extension of a previous investigation in which the behavior of nonpolar compounds in temperature-programmed gas chromatographic runs was predicted using thermodynamic (entropy and enthalpy) parameters derived from isothermal runs. In a similar manner, entropy and enthalpy parameters were determined for a Grob standard mixture of compounds with widely varying chemical characteristics. These parameters were used to predict the retention times and chromatographic behaviors of the compounds on four gas chromatography capillary columns: three that had phenyl-based stationary phases (with degrees of substitution of 0%, 5% and 50%) and one with (50%) cyanopropyl substitution. The predictions matched data empirically obtained from temperature-programmed chromatographic runs for all of the compounds extremely well, despite the wide variations in polarity of both the compounds and stationary phases. Thus, the results indicate that such simulations could greatly reduce the time and material costs of chromatographic optimizations.     

Theoretical study of the addition patterns of C60 fluorination: C60Fn (n = 1-60)

A systematic study is presented of addition patterns occurring upon fluorination of C60. We use the program SACHA, which increments the number of fluorine addends, tests all available addition sites within a given cutoff radius, and selects the most energetically stable structure for further addition on the basis of full AM1 optimizations for every isomer. The lowest energy structures are optimized at HF/3-21G level of theory. A number of distinct addition routes are predicted, based on octahedral, 'S', and 'T' addition patterns, leading both to experimentally observed C60F(n) isomers and to isomers not previously described in the literature. Furthermore the main addition routes were analyzed for C60F2n isomers, using ab initio global and local aromaticity calculations. For this, magnetizability and NICS calculations have been carried out at HF/3-21G level of theory. We show the possibility of using NICS to predict the next preferential addition site, matching the above-described addition routes.     

Porphyrins 42. Ground and excited state calculations on the isomers of free base porphine and sirohydrochlorin

Symmetry instabilities were encountered during MINDO/3 geometry optimizations of the sirohydrochlorin and porphine isomers leading to bond alternating optimal structures. Transition energies and oscillator strengths were calculated with INDO/S/CI. Our calculations predict the ground state cis and trans isomers of sirohydrochlorin to be close in energy and confirm the experimental assignment of the absorptions bands, with the cis tautomer having a red shifted spectrum.Part 41. Gouterman, M., Sayer, P., Shankland, E., Smith, J. P.: Inorg. Chem. 20, 87 (1981)     

Electronic structure and UV–Vis spectra simulation of square planar Bis(1-(4-methylphenylazo)-2-naphtol)-Transition metal complexes [M(L)2]x (M = Ni,Pd, Pt,Cu, Ag,and x = − 1, 0, + 1): DFT and TD-DFT study

Structural Chemistry - DFT/B3LYP calculations with full geometry optimizations have been carried out on 1-phenylazo-2-naphthol and their metal complexes of formula M(MePhNap)2 (M?=?Ni,...     

Ab initio prediction of the low-temperature phase diagrams in the systems CsX–LiX (X = F, Cl, Br, I)

We have calculated the low-temperature phase diagrams for the ternary alkali halides CsX–LiX (X = F, Cl, Br, I) at an ab initio level without any recourse to experimental information. The starting point of our general approach is the global exploration of the enthalpy landscapes for many different compositions in these systems. Candidates for both ordered stoichiometric modifications and crystalline solid-solution phases are identified, and their free enthalpies are computed at an ab initio level. From this the low-temperature phase diagrams are derived. We find that in all systems under investigation only crystalline ordered phases should be present, in agreement with available experimental data. Furthermore, we predict several new thermodynamically stable and metastable phases in these systems.     

An Empirically Optimized Classical Force-Field for Molecular Simulations of 2,4,6-Trinitrotoluene (TNT) and 2,4-Dinitrotoluene (DNT)

An empirical classical all-atom specific force-field for use in molecular dynamics simulations (MD) has been developed to reproduce the experimental densities and structures of trinitrotoluene (TNT) in its crystalline and liquid phases at six different temperatures, as well as its enthalpies of sublimation and fusion. The average structural parameters and partial charges were obtained from density functional theory optimizations of single molecules at the B3LYP/6-311+G** level. The other constants for the potential were adjusted in order to obtain a classical force-field, which is able to reproduce the aforementioned properties for TNT with a high degree of accuracy. This force-field was also found to predict closely the experimental densities and structures of 2,4-dinitrotoluene (2,4-DNT) in its crystalline and liquid phases as well as its enthalpy of sublimation. It was a bit less successful for its enthalpy of fusion, but it still remained reasonable, and the model mechanical properties were of the right order of magnitude. As such, this fairly simple force-field can be used for MD simulations of both TNT and 2,4-DNT nitroaromatic compounds.     

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.     

SASS: a symmetry adapted stochastic search algorithm exploiting site symmetry

A simple symmetry adapted search algorithm (SASS) exploiting point group symmetry increases the efficiency of systematic explorations of complex quantum mechanical potential energy surfaces. In contrast to previously described stochastic approaches, which do not employ symmetry, candidate structures are generated within simple point groups, such as C2, Cs, and C2v. This facilitates efficient sampling of the 3N-6 Pople's dimensional configuration space and increases the speed and effectiveness of quantum chemical geometry optimizations. Pople's concept of framework groups [J. Am. Chem. Soc. 102, 4615 (1980)] is used to partition the configuration space into structures spanning all possible distributions of sets of symmetry equivalent atoms. This provides an efficient means of computing all structures of a given symmetry with minimum redundancy. This approach also is advantageous for generating initial structures for global optimizations via genetic algorithm and other stochastic global search techniques. Application of the SASS method is illustrated by locating 14 low-lying stationary points on the cc-pwCVDZ ROCCSD(T) potential energy surface of Li5H2. The global minimum structure is identified, along with many unique, nonintuitive, energetically favorable isomers.     

The structure of the Si9H12 cluster: A coupled cluster and multi-reference perturbation theory study

Full geometry optimizations using both singles and doubles coupled cluster theory with perturbative triple excitations, CCSD(T), and second order multi-reference perturbation theory, MRMP2, have been employed to predict the structure of Si9H12, a cluster commonly used in calculations to represent the Si(100) surface. Both levels of theory predict the structure of this cluster to be symmetric (not buckled), and no evidence for a buckled (asymmetric) structure is found at either level of theory.     

Simulation of melting in crystalline polyethylene

We carry out a molecular dynamics simulation of the first stages of constrained melting in crystalline polyethylene (PE). When heated, the crystal undergoes two structural phase transitions: from the orthorhombic (O) phase to the monoclinic (M) phase, and then to the columnar (C), quasi-hexagonal, phase. The M phase represents the tendency to the parallel packing of planes of PE zigzags, and the C phase proves to be some kind of oriented melt. We follow both the transitions O→M and M→C in real time and establish that, at their beginning, the crystal tries (and fails) to pass into the partially ordered phases similar to the RI and RII phases of linear alkanes, correspondingly. We discuss the molecular mechanisms and driving forces of the observed transitions, as well as the reasons why the M and C phases in PE crystals substitute for the rotator phases in linear alkanes.     

Ab initio prediction of the low-temperature phase diagrams in the systems KBr-NaBr, KX-RbX, and LiX-RbX (X=Cl,Br)

The authors have calculated the low-temperature phase diagrams for the ternary alkali halides KBr-NaBr, KX-RbX, and LiX-RbX (X=Cl,Br) systems on the ab initio level without any recourse to experimental information. Via global exploration of the enthalpy landscapes for many different compositions in these systems, candidates for both ordered stoichiometric modifications and crystalline solid solution phases have been identified. Next, their free enthalpies were computed on ab initio level, and the respective low-temperature phase diagram has been derived. They find miscibility gaps in the systems KBr-NaBr and KX-RbX (X=Cl,Br), while in LiX-RbX (X=Cl,Br) only crystalline ordered phases should be present, in agreement with available experimental data. Furthermore, they predict several new thermodynamically stable and metastable phases in these systems.     

Conformational analysis of model compounds of vitamin D by theoretical calculations

A conformational analysis of two model compounds of vitamin D was carried out by means of theoretical computations, Ab initio calculations were carried out using the standard 6-31G* basis set at the Hartree–Fock (HF) level of theory. In addition, the Møller–Plesset (MP2) correlation treatment was applied on the simplest model. Semiempirical calculations were also performed using the AM1 Hamiltonian. The results predict stable A-ring twist forms with energies in the order of 4–6 kcal/mol relative to the global minimum, significantly higher than those reported from molecular mechanics calculations. In addition, a folded conformation was found by the HF optimizations; however, its stability is predicted to be very poor. Comparison of the theoretical results with experimental data is discussed. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1647–1655, 1997     

Cluster-assembled materials based on M12N12 (M = Al, Ga) fullerene-like clusters

We report the results of density functional theory calculations on cluster-assembled materials based on M(12)N(12) (M = Al, Ga) fullerene-like clusters. Our results show that the M(12)N(12) fullerene-like structure with six isolated four-membered rings (4NRs) and eight six-membered rings (6NRs) has a T(h) symmetry and a large HOMO-LUMO gap, indicating that the M(12)N(12) cluster would be ideal building blocks for the synthesis of cluster-assembled materials. Via the coalescence of M(12)N(12) building blocks, we find that the M(12)N(12) clusters can bind into stable assemblies by either 6NR or 4NR face coalescence, which enables the construction of rhombohedral or cubic nanoporous framework of varying porosity. The rhombohedral-MN phase is energetically more favorable than the cubic-MN phase. The M(12)N(12) fullerene-like structures in both phases are maintained and the M-N bond lengths between M(12)N(12) monomers are slightly larger than that in isolated M(12)N(12) clusters and the bulk wurtzite phases. The band analysis of both phases reveals that they are all wide-gap semiconductors. Because of the nanoporous character of these phases, they could be used for gas storage, heterogeneous catalysis, filtration and so on.     

Global optimization of parameters in the reactive force field ReaxFF for SiOH

We have used unbiased global optimization to fit a reactive force field to a given set of reference data. Specifically, we have employed genetic algorithms (GA) to fit ReaxFF to SiOH data, using an in‐house GA code that is parallelized across reference data items via the message‐passing interface (MPI). Details of GA tuning turn‐ed out to be far less important for global optimization efficiency than using suitable ranges within which the parameters are varied. To establish these ranges, either prior knowledge can be used or successive stages of GA optimizations, each building upon the best parameter vectors and ranges found in the previous stage. We have finally arrive‐ed at optimized force fields with smaller error measures than those published previously. Hence, this optimization approach will contribute to converting force‐field fitting from a specialist task to an everyday commodity, even for the more difficult case of reactive force fields. © 2013 Wiley Periodicals, Inc.     

GPU accelerated numerical simulations of viscoelastic phase separation model

We introduce a complete implementation of viscoelastic model for numerical simulations of the phase separation kinetics in dynamic asymmetry systems such as polymer blends and polymer solutions on a graphics processing unit (GPU) by CUDA language and discuss algorithms and optimizations in details. From studies of a polymer solution, we show that the GPU-based implementation can predict correctly the accepted results and provide about 190 times speedup over a single central processing unit (CPU). Further accuracy analysis demonstrates that both the single and the double precision calculations on the GPU are sufficient to produce high-quality results in numerical simulations of viscoelastic model. Therefore, the GPU-based viscoelastic model is very promising for studying many phase separation processes of experimental and theoretical interests that often take place on the large length and time scales and are not easily addressed by a conventional implementation running on a single CPU.     

药物溶解性能与溶剂分子三维静电势参数的定量关系

对一系列溶剂分子的三维静电势及其统计上的导出参数进行了计算,运用多元线性回归分析建立了扑热息痛、利多卡因、氟派啶醇和磺胺嘧啶等四种常见药物在不同溶剂中溶解度与溶剂分子三维静电势参数之间的关系。从溶剂接受质子和给质子的能力以及极性大小方面对各药物的溶解性能进行了阐述。     

Predictive power of long-range corrected functionals on the spectroscopic properties of tetrapyrrole derivatives for photodynamic therapy

Porphyrin and chlorin based compounds possess promising properties to be utilized as photosensitizers in photodynamic therapy (PDT). However, the photosensitizers available on the market today are not ideal for use in PDT, which has emphasized the need for new photosensitizers with improved photodynamic properties to be developed. Computational drug-design can be utilized in the search for improved pharmaceutical compounds, provided that the methods used are able to reproduce experimental data. In the present study we investigated, by the use of time-dependent density functional theory (TD-DFT), the performance of the long-range corrected functionals ωB97, ωB97X and ωB97XD on their ability to predict low-lying singlet excitations (>600 nm) of a set of well-known photosensitizing compounds. It was found that ωB97X reproduced the experimental red-most absorption band most satisfactorily. The use of either B3LYP, ωB97XD or M06 in geometry optimizations has a minor effect on the spectra in most cases. Calculated energy differences between the optimized singlet ground states and optimized first excited triplet states show consistent and overall higher triplet state energies for B3LYP, M06, and PBE0 compared with ωB97, ωB97X, and ωB97XD. The calculated triplet state energies are, however, sufficient to generate singlet oxygen in most cases.     

Modeling protic to dipolar aprotic solvent rate acceleration and leaving group effects in S(N)2 reactions: A theoretical study of the reaction of acetate ion with ethyl halides in aqueous and dimethyl sulfoxide solutions

The S(N)2 reactions between acetate ions and ethyl chloride, ethyl bromide, and ethyl iodide in aqueous and dimethyl sulfoxide (DMSO) solutions were theoretically investigated at an ab initio second-order M?ller-Plesset perturbation level of theory for geometry optimizations and at a fourth-order M?ller-Plesset perturbation level for energy calculations. The solvent effect was included by the polarizable continuum model using the Pliego and Riveros parametrization for DMSO and the Luque et al. scale factor for the water solution. The calculated DeltaG() values of 24.9, 20.0, and 18.5 kcal mol(-1) in a DMSO solution for ethyl chloride, ethyl bromide, and ethyl iodide are in good agreement with the estimated experimental values of 22.3, 20.0, and 16.6 kcal mol(-1), respectively. In an aqueous solution, the theoretical Delta G++ barriers of 26.9, 23.1, and 22.1 kcal mol(-1) are also in good agreement with the estimated experimental values of 26.1, 25.2, and 24.7 kcal mol(-1), respectively. The present ab initio calculations are reliable to predict the absolute and relative reactivities of ethyl halides in a DMSO solution, but in the aqueous phase, the results are less accurate. The protic to dipolar aprotic solvent rate acceleration is theoretically predicted, although this effect is underestimated. We suggest that further improvement of the present results could be obtained by including liquid-phase optimization in both solvents and treating specific solvation by water molecules for the reaction in the aqueous phase.