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1.
《Journal of computational chemistry》2017,38(13):949-956
We present a computational study of magnetic‐shielding and quadrupolar‐coupling tensors of 43Ca sites in crystalline solids. A comparison between periodic and cluster‐based approaches for modeling solid‐state interactions demonstrates that cluster‐based approaches are suitable for predicting 43Ca NMR parameters. Several model chemistries, including Hartree–Fock theory and 17 DFT approximations (SVWN, CA‐PZ, PBE, PBE0, PW91, B3PW91, rPBE, PBEsol, WC, PKZB, BMK, M06‐L, M06, M06‐2X, M06‐HF, TPSS, and TPSSh), are evaluated for the prediction of 43Ca NMR parameters. Convergence of NMR parameters with respect to basis sets of the form cc‐pVXZ (X = D, T, Q) is also evaluated. All DFT methods lead to substantial, and frequently systematic, overestimations of experimental chemical shifts. Hartree–Fock calculations outperform all DFT methods for the prediction of 43Ca chemical‐shift tensors. © 2017 Wiley Periodicals, Inc. 相似文献
2.
Stefan Maintz Volker L. Deringer Andrei L. Tchougréeff Richard Dronskowski 《Journal of computational chemistry》2013,34(29):2557-2567
Quantum‐chemical computations of solids benefit enormously from numerically efficient plane‐wave (PW) basis sets, and together with the projector augmented‐wave (PAW) method, the latter have risen to one of the predominant standards in computational solid‐state sciences. Despite their advantages, plane waves lack local information, which makes the interpretation of local densities‐of‐states (DOS) difficult and precludes the direct use of atom‐resolved chemical bonding indicators such as the crystal orbital overlap population (COOP) and the crystal orbital Hamilton population (COHP) techniques. Recently, a number of methods have been proposed to overcome this fundamental issue, built around the concept of basis‐set projection onto a local auxiliary basis. In this work, we propose a novel computational technique toward this goal by transferring the PW/PAW wavefunctions to a properly chosen local basis using analytically derived expressions. In particular, we describe a general approach to project both PW and PAW eigenstates onto given custom orbitals, which we then exemplify at the hand of contracted multiple‐ζ Slater‐type orbitals. The validity of the method presented here is illustrated by applications to chemical textbook examples—diamond, gallium arsenide, the transition‐metal titanium—as well as nanoscale allotropes of carbon: a nanotube and the fullerene. Remarkably, the analytical approach not only recovers the total and projected electronic DOS with a high degree of confidence, but it also yields a realistic chemical‐bonding picture in the framework of the projected COHP method. © 2013 Wiley Periodicals, Inc. 相似文献
3.
Chang Kon Kim Jongok Won Hoon Sik Kim Yong Soo Kang Hong Guang Li Chan Kyung Kim 《Journal of computational chemistry》2001,22(8):827-834
The formation and physicochemical properties of polymer electrolytes strongly depend on the lattice energy of metal salts. An indirect but efficient way to estimate the lattice energy through the relationship between the heterolytic bond dissociation and lattice energies is proposed in this work. The heterolytic bond dissociation energies for alkali metal compounds were calculated theoretically using the Density Functional Theory (DFT) of B3LYP level with 6‐311+G(d,p) and 6‐311+G(2df,p) basis sets. For transition metal compounds, the same method was employed except for using the effective core potential (ECP) of LANL2DZ and SDD on transition metals for 6‐311+G(d,p) and 6‐311+G(2df,p) calculations, respectively. The dissociation energies calculated by 6‐311+G(2df,p) basis set combined with SDD basis set were better correlated with the experimental values with average error of ca. ±1.0% than those by 6‐311+G* combined with the LANL2DZ basis set. The relationship between dissociation and lattice energies was found to be fairly linear (r>0.98). Thus, this method can be used to estimate the lattice energy of an unknown ionic compound with reasonably high accuracy. We also found that the dissociation energies of transition metal salts were relatively larger than those of alkaline metal salts for comparable ionic radii. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 827–834, 2001 相似文献
4.
Jaszewski AR Petrie S Pace RJ Stranger R 《Chemistry (Weinheim an der Bergstrasse, Germany)》2011,17(20):5699-5713
Density functional theory (DFT) and time‐dependent DFT (TDDFT) calculations are reported on three sets of isomeric models of the {Mn4/Ca} water‐oxidizing complex of photosystem II (PS II), which share the general formula [CaMn4O4(N2C3H4)(RCOO)6]q?(H2O)n (R=H, CH3; q=?1, 0, +1, +2; n=3, 4, 5, 6, 7). Comparison with the full range of available data on Mn K‐edge X‐ray absorption energy values determined for the photosystem allows us to validate the structures that correspond to the particular S states and to determine their Mn oxidation patterns. By using a new TDDFT procedure, it is shown that variations in the absolute K‐edge energy values for a particular S state, reported by different research groups, can be quantitatively explained by different geometries adopted by the Mn cluster, which demonstrates flexibility in the position of the fourth ‘dangling’ Mn atom in relation to a cubane structure created by the Ca atom and the three other Mn atoms. Computational results show that each step of the S cycle occurs by removal of one electron directly from the Mn cluster. This Mn‐centered oxidation still agrees with the small difference observed experimentally between the K‐edge energy values of the S2 and S3 states of the photosystem, thus resolving a controversy as to whether this represents ligand‐centered or metal‐centered oxidation. The overall oxidation state of Mn atoms in the tetramanganese cluster during functional turnover changes from 2.75 for S0, 3.00 for S1, and 3.25 for S2 up to 3.50 for the S3 state, which is systematically 0.50 lower than the previously proposed oxidation states of the cluster. The calculations give insight into why these earlier, purely empirical, assignments of the Mn oxidation levels in PS II could be in error. 相似文献
5.
Rapid QM/MM approach for biomolecular systems under periodic boundary conditions: Combination of the density‐functional tight‐binding theory and particle mesh Ewald method
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A quantum mechanical/molecular mechanical (QM/MM) approach based on the density‐functional tight‐binding (DFTB) theory is a useful tool for analyzing chemical reaction systems in detail. In this study, an efficient QM/MM method is developed by the combination of the DFTB/MM and particle mesh Ewald (PME) methods. Because the Fock matrix, which is required in the DFTB calculation, is analytically obtained by the PME method, the Coulomb energy is accurately and rapidly computed. For assessing the performance of this method, DFTB/MM calculations and molecular dynamics simulation are conducted for a system consisting of two amyloid‐β(1‐16) peptides and a zinc ion in explicit water under periodic boundary conditions. As compared with that of the conventional Ewald summation method, the computational cost of the Coulomb energy by utilizing the present approach is drastically reduced, i.e., 166.5 times faster. Furthermore, the deviation of the electronic energy is less than . © 2016 Wiley Periodicals, Inc. 相似文献
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Characterizing the Intermediates Compound I and II in the Cytochrome P450 Catalytic Cycle with Nonlinear X‐ray Spectroscopy: A Simulation Study
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Cytochrome P450 enzymes are an important family of biocatalysts that oxidize chemically inert C?H bonds. There are many unresolved questions regarding the catalytic reaction intermediates, in particular P450 Compound I (Cpd‐I) and II (Cpd‐II). By using simple molecular models, we simulate various X‐ray spectroscopy signals, including X‐ray absorption near‐edge structure (XANES), resonant inelastic X‐ray scattering (RIXS), and stimulated X‐ray Raman spectroscopy (SXRS) of the low‐ and high‐spin states of Cpd‐I and II. Characteristic peak patterns are presented and connected to the corresponding electronic structures. These X‐ray spectroscopy techniques are complementary to more conventional infrared and optical spectroscopy and they help to elucidate the evolving electronic structures of transient species along the reaction path. 相似文献
8.
Herrmann H Fillol JL Wadepohl H Gade LH 《Angewandte Chemie (International ed. in English)》2007,46(44):8426-8430
9.
In this theoretical work, 22 alcohols and their geometric structure properties have been investigated employing quantum chemical methods to calculate the C? OH equilibrium bond distances and bond dissociation energies (BDEs). Since DFT methods have been researched to have low basis sets sensitivity for small and medium molecules in our previous work (Zhao et al., J Mol Struct, 2006, 766, 87), 22 title compounds have been studied by employing the hybrid density functional theory (B3LYP, B3PW91, B3P86, PBE1PBE) in conjunction with the 6‐311G** basis set and the complete basis set (CBS–Q) method. Comparison with the available experimental data shows that CBS–Q and B3P86 methods calculated results agree very well with the experimental values, with the average absolute errors of 1.3 kcal/mol and 3.5 kcal/mol, respectively. So considering the expensive computational time, CBS–Q method can be chosen as a satisfactory method of predicting the accurate BDEs for removal of the OH group in small and medium size alcohols. And B3P86 method may give accurate BDEs for larger alcohols we haven't studied. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011 相似文献
10.
The approximate density‐functional tight‐binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free‐energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) electron‐induced repair of a DNA lesion. Also discussed is the further development of the framework, regarding mostly the options for parallelization. © 2015 Wiley Periodicals, Inc. 相似文献
11.
Fukuzawa K Kitaura K Uebayasi M Nakata K Kaminuma T Nakano T 《Journal of computational chemistry》2005,26(1):1-10
We have theoretically examined the relative binding affinities (RBA) of typical ligands, 17beta-estradiol (EST), 17alpha-estradiol (ESTA), genistein (GEN), raloxifene (RAL), 4-hydroxytamoxifen (OHT), tamoxifen (TAM), clomifene (CLO), 4-hydroxyclomifene (OHC), diethylstilbestrol (DES), bisphenol A (BISA), and bisphenol F (BISF), to the alpha-subtype of the human estrogen receptor ligand-binding domain (hERalpha LBD), by calculating their binding energies. The ab initio fragment molecular orbital (FMO) method, which we have recently proposed for the calculations of macromolecules such as proteins, was applied at the HF/STO-3G level. The receptor protein was primarily modeled by 50 amino acid residues surrounding the ligand. The number of atoms in these model complexes is about 850, including hydrogen atoms. For the complexes with EST, RAL, OHT, and DES, the binding energies were calculated again with the entire ERalphaLBD consisting of 241 residues or about 4000 atoms. No significant difference was found in the calculated binding energies between the model and the real protein complexes. This indicates that the binding between the protein and its ligands is well characterized by the model protein with the 50 residues. The calculated binding energies relative to EST were very well correlated with the experimental RBA (the correlation coefficient r=0.837) for the ligands studied in this work. We also found that the charge transfer between ER and ligands is significant on ER-ligand binding. To our knowledge, this is the first achievement of ab initio quantum mechanical calculations of large molecules such as the entire ERalphaLBD protein. 相似文献
12.
Roth C Peppel T Fumino K Köckerling M Ludwig R 《Angewandte Chemie (International ed. in English)》2010,49(52):10221-10224
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Synthesis and Characterization of Ba[CoSO]: Magnetic Complexity in the Presence of Chalcogen Ordering
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Dr. Martin Valldor Dr. Ulrich K. Rößler Dr. Yurii Prots Dr. Chang‐Yang Kuo Dr. Jen‐Che Chiang Dr. Zhiwei Hu Dr. Tun‐Wen Pi Prof. Dr. Rüdiger Kniep Prof. Dr. Liu Hao Tjeng 《Chemistry (Weinheim an der Bergstrasse, Germany)》2015,21(30):10821-10828
Barium thio‐oxocobaltate(II), Ba[CoS2/2O2/2], was synthesized by the reaction of equimolar amounts of BaO, Co, and S in closed silica ampoules. The title compound (Cmcm, a=3.98808(3), b=12.75518(9), c=6.10697(4) Å) is isostructural to Ba[ZnSO]. The use of soft X‐ray absorption spectroscopy confirmed that cobalt is in the oxidation state +2 and tetrahedrally coordinated. Its coordination consists of two sulfur and two oxygen atoms in an ordered fashion. High‐temperature magnetic susceptibility data indicate strong low‐dimensional spin–spin interactions, which are suggested to be closely related to the layer‐type crystal structure and perhaps the ordered distribution of sulfur and oxygen. Antiferromagnetic ordering below TN=222 K is observed as an anomaly in the specific heat, coinciding with a significant lowering of the magnetic susceptibility. Density functional theory calculations within a generalized‐gradient approximation (GGA)+U approach identify an antiferromagnetic ground state within the square‐like two‐dimensional layers of Co, and antiferromagnetic correlations for nearest and next nearest neighbors along bonds mediated by oxygen or sulfur. However, this magnetic state is subject to frustration by relatively strong interlayer couplings. 相似文献
15.
In this work, we devote to explore excited‐state intramolecular proton transfer (ESIPT) behavior for a novel fluorescent molecule naphthalimide‐based 2‐(2‐hydroxyphenyl)‐benzothiazole (HNIBT) [New J. Chem. 2019, 43, 9152.] in toluene and methanol (MeOH) solvents. Exploring weak interactions, stable HNIBT‐enol, and HNIBT‐MeOH‐enol complex can be found in S0 state via TDDFT/B3LYP/6‐311+G(d,p) level. Given photoexcitation, intramolecular hydrogen bond O1? H2···N3 of HNIBT‐enol and HNIBT‐MeOH‐enol is dramatically enhanced, which offers impetus for facilitates ESIPT reaction. After repeated comparisons, we verify the unavailability of intermolecular hydrogen bonding effects between HNIBT‐enol and MeOH molecules. In view of excitation, HOMO (π) → LUMO (π*) transition and the changes of electronical densities indeed impulse ESIPT tendency. Via constructing potential energy curves (PECs), for both HNIBT‐enol and HNIBT‐MeOH‐enol complex, the ESIPT could only occur along with intramolecular hydrogen bond O1? H2···N3. Through comparison, the potential barrier falls from 4.124 kcal/mol (HNIBT‐enol) to 2.132 kcal/mol (HNIBT‐MeOH‐enol). Therefore, we confirm that the ESIPT of the HNIBT system happens more easily in the MeOH solvent compared with the toluene solvent. 相似文献
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Pierre Mignon Stefan Loverix Jan Steyaert Paul Geerlings 《International journal of quantum chemistry》2004,99(1):53-58
Experimentally, the functional assessment of amino acid side chains in proteins is carried out by comparing parameters such as binding constants for the wild‐type protein and a mutant protein in which the considered side chain is deleted. In the present study, we apply a density functional theory (DFT) methodology to obtain changes in binding energy upon mutations in the enzyme ribonuclease T1. Mutant structures were either taken directly from crystallographic data (“in vivo”) allowing for conformational changes upon mutation, or derived from the wild‐type (“in silico”). Excluding entropic contributions, the computed interaction energy changes upon mutation in vivo correlate qualitatively well with experimental binding free energy changes. In contrast, the in silico approach does not perform as well, especially for residues that contribute largely to binding. Subsequently, we assessed the applicability of the in vivo approach by analyzing the functional cooperativity between pairs of side chains. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004 相似文献
18.
Cyclic acyl phosphoramidates (CAPAs) are important components in several fundamental biological reactions such as protein synthesis and phosphorylation. These structures are particularly interesting in the nucleotide pro‐drug approach, Pro‐Tide, since they are putative intermediates in one of the hydrolysis steps required for activation. The central role played by the amino acid carboxylate function suggests first the formation of a cyclic mixed phosphorus anhydride, rapidly followed by water attack. To investigate such speculations, we performed quantum mechanical calculations using the B3LYP/6‐311+G** level of theory for the plausible mechanisms of action considered. In the five‐membered ring case, transition state theory demonstrated how the overall, gas‐phase, mechanism of action could be split into two in‐line addition–elimination (A–E) steps separated by a penta‐coordinate phosphorane intermediate. The difference between five‐membered and six‐membered ring first A–E was also explored, revealing a single step, unimolecular reaction for the six‐membered ring A–E profile. Implicit solvent contribution further confirmed the importance of CAPAs as reactive intermediates in such kind of reactions. Lastly, the second A–E pathway was analyzed to understand the complete pathway of the reaction. This analysis is the first attempt to clarify the putative mechanism of action involved in the activation of Pro‐Tides and casts light also on the possible mechanism of action involved in primordial protein syntheses, strengthening the hypothesis of a common cyclic mixed phosphorus anhydride species as a common intermediate. © 2012 Wiley Periodicals, Inc. 相似文献
19.
Abu Md. Asaduzzaman Guy A. G. Chappellaz Georg Schreckenbach 《Journal of computational chemistry》2012,33(31):2492-2497
It has been proposed that iodine binding to dyes may actually decrease the cell efficiency of a dye‐sensitized solar cell. A previous experimental study showed that a two‐atom change from oxygen to sulfur increased recombination of iodine with injected electrons by a factor of approximately 2. Here, it is shown that iodine binding is a plausible explanation for this effect. The steric and conjugation effects are quantified separately using a set of model compounds. Quantum‐chemical calculations show that elongation of the hydrocarbon chain has only an insignificant effect on the iodine and bromine binding to the chalcogen atoms (O, S, Se). The conjugation, however, significantly disfavors the iodine and bromine interaction. Iodine and bromine binding to the dye and model compounds containing sulfur is significantly more favorable than to their oxygen containing counterparts. Bromine binding to dyes is shown to be stronger than that of iodine. Accordingly, bromine binding to dyes may contribute significantly to the observed lower efficiencies in cells using Br/Br? as the redox couple. © 2012 Wiley Periodicals, Inc. 相似文献
20.
Kavathekar R Khire S Ganesh V Rahalkar AP Gadre SR 《Journal of computational chemistry》2009,30(7):1167-1173
A web-interface for geometry optimization of large molecules using a linear scaling method, i.e., cardinality guided molecular tailoring approach (CG-MTA), is presented. CG-MTA is a cut-and-stitch, fragmentation-based method developed in our laboratory, for linear scaling of conventional ab initio techniques. This interface provides limited access to CG-MTA-enabled GAMESS. It can be used to obtain fragmentation schemes for a given spatially extended molecule depending on the maximum allowed fragment size and minimum cut radius values provided by the user. Currently, we support submission of single point or geometry optimization jobs at Hartree-Fock and density functional theory levels of theory for systems containing between 80 to 200 first row atoms and comprising up to 1000 basis functions. The graphical user interface is built using HTML and Python at the back end. The back end farms out the jobs on an in-house Linux-based cluster running on Pentium-4 Class or higher machines using an @Home-based parallelization scheme (http://chem.unipune.ernet.in/ approximately tcg/mtaweb/). 相似文献