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1.
K. J. Jalkanen J. D. Gale G. J. Jalkanen D. F. McIntosh A. A. El-Azhary G. M. Jensen 《Theoretical chemistry accounts》2008,119(1-3):211-229
In this work we present the experimental vibrational absorption (VA), vibrational circular dichroism (VCD) and Raman spectra
for (+)-trans-1(S),2(S)-dicyanocyclopropane and its dideuterio derivative, trans-1(S),2(S)-dicyano-1(S),2(S)-dideuteriocyclopropane, along with VA, VCD, Raman and Raman optical activity (ROA) spectral simulations.
Here we investigate the applicability of various local and non-local exchange-correlation (XC) functionals, hybrids and meta-hybrids
to reproduce the vibrational spectra of this strained ring system, which also bears two cyano groups. At the highest level
of theory, B3PW91/ aug-cc-pVTZ, we also investigated the trans-, cis- and gem-dicyanocyclopropane (trans-, cis-, and gem-DCCP), cyanocyclopropane (CCP) and the parent molecule cyclopropane (CP). In doing so we have investigated the electronic
effects (coupling) between the cyano groups and the cyclopropane ring. In addition to providing an interpretation of the experimentally
observed vibrational spectra for these molecules, this work also provides benchmark calculations for other methods, especially
semi-empirical based wave function and density functional theory (DFT) based methods, such as SCC-DFTB and PM6. For the semi-empirical
DFT based methods to be used for 3-membered ring systems, one ought to document their reliability for systems which were not
used in the parameterization. The small 3- and 4-membered ring systems are good test systems because they contain non-standard
bonding, which may be difficult to determine accurately with the approximations used in the SCC-DFTB and other semi-empirical
methods. Like molecular mechanics force fields, semi-empirical methods, based on DFT and wave function quantum mechanics (WFQM),
must be benchmarked against high level ab initio and DFT calculations and experimental data. In addition to bonding, the changes
in the electric dipole moment, magnetic dipole moment, electric dipole-electric dipole polarizability, electric dipole-magnetic
dipole polarizability and electric dipole-electric quadrupole polarizability with respect to nuclear displacement and nuclear
velocity can be determined by the VA, VCD, Raman and ROA intensities. Hence it is important that the semi-empirical based
DFT and wave function methods not only be parameterized to determine energies, gradients and Hessians, but also the electric
and magnetic moments and their derivatives that determine the electronic and magnetic properties of these molecules and their
interactions with matter and radiation. This will allow biochemists, biophysicists, molecular biologists, and physical biologists
to use experimental and theoretical VA, VCD, Raman and ROA spectroscopies to probe biophysical and biochemical function and
processes at the molecular level.
Festschrift in Honor of Philip J. Stephens’ 65th Birthday. 相似文献
2.
使用密度泛函理论B3LYP方法和6-31G(d,p)、6-31＋G(d,p)、6-311G(d,p)及6-311＋G(d,p)基组,分别对2-C5H10＋和1-C5H10＋的各种构象进行了几何构型优化,并用B3LYP/6-311G(d,p)进行了频率分析计算.计算预言1-C5H10＋具有非平面构型,与以往报导的从头算计算结论相反.在两个自由基阳离子的各种构象的B3LYP几何构型上,进行了B3LYP和UMP2(full)方法的超精细偶合常数计算,得到了比以往更好的结果. 相似文献
3.
K. J. Jalkanen Julian D. Gale P. R. Lassen L. Hemmingsen A. Rodarte I. M. Degtyarenko R. M. Nieminen S. Brøgger Christensen M. Knapp-Mohammady S. Suhai 《Theoretical chemistry accounts》2008,119(1-3):177-190
In this work we present the experimental and theoretical vibrational absorption (VA) and the theoretical vibrational circular
dichroism (VCD) spectra for aframodial. In addition, we present the theoretical VA and VCD spectra for the diasteriomers of
aframodial. Aframodial has four chiral centers and hence has 24 = 16 diasteriomers, which occur in eight pairs of enantiomers. In addition to the four chiral centers, there is an additional
chirality due to the helicity of the entire molecule, which we show by presenting 12 configurations of the 5S,8S,9R,10S enantiomer
of aframodial. The VCD spectra for the diasteriomers and the 12 configurations of one enantiomer are shown to be very sensitive
not only to the local stereochemistry at each chiral center, but in addition, to the helicity of the entire molecule. Here
one must be careful in analyzing the signs of the VCD bands due to the ‘non-chiral’ chromophores in the molecule, since one
has two contributions; one due to the inherent chirality at the four chiral centers, and one due to the chirality of the side
chain groups in specific conformers, that is, its helicity. Theoretical simulations for various levels of theory are compared
to the experimental VA recorded to date. The VCD spectra simulations are presented, but no experimental VCD and Raman spectra
have been reported to date, though some preliminary VCD measurements have been made in Stephens’ lab in Los Angeles. The flexible
side chain is proposed to be responsible for the small size of the VCD spectra of this molecule, even though the chiral part
of the molecule is very rigid and has four chiral centers. In addition to VCD and Raman measurements, Raman optical activity
(ROA) measurements would be very enlightening, as in many cases bands which are weak in both the VA and VCD, may be large
in the Raman and/or ROA spectra. The feasibility of using vibrational spectroscopy to monitor biological structure, function
and activity is a worthy goal, but this work shows that a careful theoretical analysis is also required, if one is to fully
utilize and understand the experimental results. The reliability, reproduceability and uniqueness of the vibrational spectroscopic
experiments and the information which can be gained from them is discussed, as well as the details of the computation of VA,
VCD and Raman (and ROA) spectroscopy for molecules of the complexity of aframodial, which have multiple chiral centers and
flexible side chains.
Festschrift in Honor of Philip J. Stephens’ 65th Birthday. 相似文献
4.
Ab initio HF, HF + MP2, LDA DFT, BLYP DFT, and B3LYP DFT calculations are compared in the case of 19 homopolypeptides in their β pleated sheet conformation. The results show that the B3LYP method provides good results for the fundamental gaps, as compared with the values estimated on the basis of available UV spectra and intermediate exciton calculations for PolyGly and PolyAla. The HF method gives the best agreement, using Koopman's theorem for the ionization potential, taking the calculated VBmax values in the HF case if one compares them with the experimental ionization potentials of the 19 amino acids measured by mass spectroscopy. Finally, how these methods might be improved to determine the most stable conformations of the homopolypeptides is outlined. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004 相似文献
5.
We have investigated the performance of the OLYP and O3LYP density functionals for predicting atomic excitation energies and ionization potentials, and bond dissociation energies, geometries, and vibrational frequencies for selected first-row transition metal compounds, including hydrides (MH) and singly charged methylene and methyl cations. The OLYP and O3LYP functionals are similar to the well-known BLYP and B3LYP functionals, respectively, but use a new optimized exchange functional (OPTX) developed by Handy and Cohen (Mol Phys 2001, 99, 403) in place of the standard B88 exchange. A previous study by us on organic reactions (J Chem Phys 2002, 117, 1331) indicated that both OLYP and O3LYP gave results for heats of reaction and barrier heights that were overall superior to those using the popular B3LYP functional. For transition metals, however, although OLYP is overall superior to BLYP for molecular calculations, it is inferior to B3LYP. O3LYP provides results for molecules of about the same quality as B3LYP. For atomic excitation and 4s ionization energies, unless relativistic effects are included, OLYP and O3LYP are clearly worse than both BLYP and B3LYP. There is thus no real incentive to use either OLYP or O3LYP in place of B3LYP for calculations involving first-row transition metals. 相似文献
6.
From the changes in energy band, density of state (DOS) and electronic structure calculated by the DFT/B3LYP method, the conductivity of carbon doped boron‐nitride nanotube (BNNT), which is formed by C‐C bond substituting B‐N bond, was discussed. The results indicate that the substitution will strengthen the conductivity of the tube, and its semi‐conductivity might be adjusted by controlling the substitution. 相似文献
7.
Reduction of tetranuclear heterometallic complex Mo2Mg2 was simulated using the B3LYP and PBE density functional methods. The results of geometry calculations of the initial complex [MoVIO2Mg(MeOH)2(OMe)4]2 and a partially reduced MoV complex are in good agreement with experimental data. The reduced MoIII complex is characterized by a decrease in the binding energy of aqua ligands. Structural rearrangement of the complex with release of a coordination position at the Mo atoms requires small energy expenditure. One can assume that the reduction of the polynuclear complex causes overcrowding of its coordination sphere, which favors formation of dinitrogen complexes. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 441–457, March, 2008. 相似文献
8.
用密度泛函理论(DFT)B3LYP方法,在3-21G水平上系统研究了C~3~6二聚体(C~3~6)~2的可能的稳定结构及其稳定性。结果表明,两个C~3~6的腰带六元环面对面以两根C－C键连接具有D~2~h对称性的结构的能量最低。在所研究的二聚体(C~3~6)~2中,C~3~6笼间键长在0.151～0.169nm之间,表明C~3~6单体间均以共价键结合。(C~3~6)~2的稳定性以及笼间键长与成键原子的位置密切相关。本文还给出了计算所得的电子结构,并讨论了其对(C~3~6)~2性质的影响。 相似文献
9.
Theoretical study on the molecular structures of X-, α-, and β-types of lithium phthalocyanine dimer
Sumimoto M Kawashima Y Yokogawa D Hori K Fujimoto H 《Journal of computational chemistry》2011,32(14):3062-3067
We report here the results from theoretical calculations of the potential energy curves, the geometry optimizations, and the electronic structures for three dimers of lithium phthalocyanine (LiPc) by using three types of functional systems: PBE1PBE, B3LYP, and M06. The results were discussed in comparison with those obtained for the dimers of magnesium phthalocyanine (MgPc). The long-range dispersive interactions were considered in part using these functional systems in the increasing order of PBE1PBE, B3LYP, and M06. The mechanism whereby the dispersive interactions affect the geometric and electronic structures of the LiPc and MgPc dimers is discussed. The calculated results provide insight into the computational methods for both open- and closed-shell metal phthalocyanine (MPc) dimers: Although the PBE1PBE and B3LYP functional systems cannot evaluate a weak dispersion interaction appropriately, the M06 functional can estimate a weak dispersion interaction well in both open- and closed-shell MPc dimers. Basis set superposition error (BSSE) corrections play an important role for the quantitative analysis; however, the calculation results without BSSE corrections may be sufficient for the qualitative discussion on the properties of these dimers such as geometries, stabilities, electronic structures, and so on. 相似文献
10.
１９９８年,李远哲等［１］对ＨＣＳ自由基进行了傅里叶变换毫米波光谱实验研究,测定了质子的超精细耦合常数Ａ（Ｈ）为１２７．４２７ＭＨｚ．他们注意到此值远小于ＨＣＯ自由基的Ａ（Ｈ）值,并认为这与ＨＣＳ的键角比ＨＣＯ的键角大有关．我们用密度泛函理论中的（Ｕ）Ｂ３ＬＹＰ［２,３］方法对ＨＣＳ及有关的ＨＣＯ、ＨＳＩＳ和ＨＳＩＯ自由基进行了计算研究．本研究结果表明：Ｂ３ＬＹＰ方法计算的ＨＣＳ的Ａ（Ｈ）与实验值非常一致;键角的大小不足以解释ＨＣＳ的Ａ（Ｈ）值远小于ＨＣＯ这一事实;用自旋密度却可简明地加以解释．… 相似文献
11.
In this work, we examine the performance of XYG3, a newly developed doubly hybrid density functional (Zhang, Xu, and Goddard III, Proc Natl Acad Sci USA 2009, 106, 4963), to calculate covalent bond dissociation enthalpy (BDE). We use 5 atoms, 32 molecular radicals, and 116 closed-shell molecules to set up 142 bond dissociation reactions. For the total of 148 heats of formation (HOFs) and 142 BDEs, XYG3 leads to mean absolute deviations (MADs) of 1.45 and 1.87 kcal/mol, respectively. In comparison with some other functionals, MADs for HOFs are 2.31 (M06-2X), 2.98 (B2PLYP-D), 3.04 (BMK), 3.96 (B3LYP), 4.47 (B2PLYP), 5.42 (B2GP-PLYP), 6.46 (PBE0), and 29.93 kcal/mol (B3P86), and the corresponding errors for BDEs are 2.06 (M06-2X), 2.25 (BMK), 2.51 (B2PLYP-D), 2.89 (B2GP-PLYP), 3.30 (B3P86), 3.44 (B2PLYP), 3.87 (PBE0), and 6.14 kcal/mol (B3LYP). 相似文献
12.
The hydrolytic deamination mechanism of adenosine to produce inosine was studied using density functional method on two models.
One is adenine and the other is adenosine. Optimized geometries of reactants, intermediates, transition states, and products
were determined at B3LYP/6-311G(d,p) level. IRC calculations were performed on the transition states to verify whether it
is the real transition state that connects the corresponding intermediates. Single point calculations were carried out on
the previous optimized geometries obtained during IRC calculations. Four pathways have been determined for the hydrolytic
deamination of adenosine. Pathway d is the most favorable pathway. In this pathway a tetra-coordinated intermediate is formed through hydrolysis reaction, then
the deamination reaction takes place, which causes the cleavage of C6–N10 bond and the creation of C=O bond. Unlike the deamination
of adenine, the attacking side of water molecule has effect on the deamination of adenosine. The energy barriers of adenosine
deamination are a little higher than those of adenine deamination.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
13.
使用密度泛函理论B3LYP方法和6-31G(d,p),6-31+G(d,p),6-311G(d,p)及6- 311+G(d,p)基组,分别对1-C_6H_(12)~+,2-C_6H_(12)~+和3-C_6H_(12)~+的各种构 象进行了几何构型优化,并在B3LYP/6-311G(d,p)水平上进行了频率分析计算,在 各优化构型上,使用B3LYP和MP2(full)方法进行了超精细结构的计算。计算的3- C_6H_(12)~+的超精细偶合常数比以往的计算结果更好;1-C_6H_(12)~+和2-C_6H_ (12)~+的超精细偶合常数目前尚无实验数据报道,本计算预言了它们的超精细偶合 常数和最稳定构型。 相似文献
14.
A series of N‐methyl‐3,4‐fulleropyrrolidine (NMFP) derivatives were designed by selecting different π‐conjugated linkers and electron‐donating groups as D‐π‐A and D‐A systems. The optimised structures and photo‐physical properties of NMFP and its derivatives have been determined using density functional theory (DFT) and time‐dependent density functional theory (TD‐DFT) methods with the B3LYP functional and the 6‐31G basis set. According to the computation analysis, both the π‐conjugated linkers and the electron‐donating groups can influence the electronic and photo‐physical properties of the NMFP derivatives. Our calculated results demonstrated that the electron‐donating groups, with significant electron‐donating ability, had the tendency to increase the highest occupied molecular orbital (HOMO) energy. The π‐conjugated linkers with lower resonance energy decreased the lowest occupied molecular orbital (LUMO) energy and caused a significant decrease in the energy gap (Eg) between the EHOMO and ELUMO. A Natural Bond Orbital (NBO) analysis examines the effect of the electron‐donating group, π conjugated linker, and electron‐withdrawing group for these NMFP derivatives. For the NMFP derivatives, a projected density of state (PDOS) analysis demonstrated that the electron density of HOMO and LUMO are concentrated on the electron‐donating group and the π‐conjugated linker, respectively. A TD‐DFT/B3LYP calculation was performed to calculate the electronic absorption spectra of these NMFP derivatives. Both the electron‐donating group and the π‐conjugated linker contribute to the major absorption peaks, which are assigned as HOMO to LUMO transitions and are red‐shifted relative to those of non‐substituted NMFP. 相似文献
15.
Ab initio B3LYP crystal orbital (CO) calculations have been performed on the 19 homopolypeptides (PolyGly, PolyAla, PolySer, PolyThre, PolyLeu, PolyiLeu, PolyVal, PolyAspAc, PolyAsp, PolyGlutAc, PolyGlut, PolyHist, PolyProl, PolyCyst, PolyMeth, PolyTyr, PolyPhenAla, PolyArg, and PolyLys) in their β pleated sheet conformation. Keeping the main chain conformation fixed as in PolyGly, the side chain geometries were optimized. For the calculation 2n+1 different k points were used with n = 8 for the case of simpler and n = 10 for more complicated side chains. The basis set applied was the double ζ one of Clementi. According to the results obtained, the conduction bands are shifted upward and the valance band downward, compared with the results of previous BLYP 1 and LDA 7 CO calculations. The bandwidths are similar to the previous cases. The band edges are in many cases not at the endpoints of the first Brillouin zones, causing nonmonotonous dispersion of both the conduction bands (CB) and the valance bands (VB), respectively. The fundamental gap values due to the upward shifts of the CB and downward shifts of the VB are substantially larger than in the case of our previous DFT CO calculations (values 6.0–7.0 eV). They are very close to the gap values, which can be estimated on the basis of experimental ultraviolet (UV) spectra of some homopolypeptides and on the basis of intermediate exciton theoretical calculations (6.5–7.5 eV). These surprisingly good results for the gaps are due to the compensation of errors (LDA or BLYP gives too small and simple HF provides too large gap values) in the B3LYP method. The admixture of the exact HF exchange with a weight of 0.19 obviously compensates the self interaction error occurring in the LDA or BLYP methods. This article discusses whether/how this result could be established by other B3LYP CO calculations on simple polymer chains and on stacked systems (e.g., nucleotide base stacks). Furthermore, a comparative analysis of the ground state DFT methods, the HF method and of the optimized effective potential method could throw more light on our successful theoretical results for the gaps of the homopolypeptides. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004 相似文献
16.
Recently, we proposed the X1 method which combines the B3LYP/6‐311+G(3df,2p)//B3LYP/6‐311+G(d,p) method with a neural network correction for an accurate yet efficient prediction of heats of formation (Wu and Xu, J Chem Phys 2007, 127, 214105). In this contribution, we discuss in detail how to set up the X1 neural network. We give examples, showing how to apply the X1 method and how the applicability of X1 can be extended. The overall mean absolute deviation of the X1 method from experiment for the 488 heats of formation is 1.52 kcal/mol compared with 9.44 kcal/mol for the original B3LYP results. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 相似文献
17.
Maria Rudbeck 《International journal of quantum chemistry》2012,112(11):2435-2439
The addition of extravalence, polarization and diffuse functions, were studied in order to conclude how they affect the P? O stretching frequencies of several biological relevant phosphate molecules. The results show that the polarization and the diffuse functions have opposite effects on the frequencies: the polarization functions downshift while the diffuse functions upshift the frequencies. The effect of the valence functions was more difficult to interpret. The effect of the conductor‐like screening model (CPCM)‐continuum model was also studied. The results show that the CPCM‐continuum model has a substantial effect on the frequencies for these small molecules. The continuum model's efficiency is mainly due to its effect on the geometries and not on the frequencies. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012 相似文献
18.
Gustavo R. Silva Itamar Borges Jose D. Figueroa‐Villar 《International journal of quantum chemistry》2005,105(3):260-269
A systematic study of the oxime HI‐6 [1‐(2‐hydroxyiminomethyl‐1‐pyridinium)‐1‐(4‐carboxy‐aminopyridinium)dimethyl ether] hydrochloride, which is one of the most promising antidotes against soman intoxication, was carried out using density functional theory with the B3LYP (Becke, Lee, Yang, and Parr) method and the 6‐31+G*, 6‐31+G*, and 6‐31+G** basis sets. Rotational barriers, equilibrium geometries, and charge distributions were calculated in order to investigate the role of the side chain for the larger oximes used as antidotes in the treatment of neurotoxic organophosphate poisoning. Also reported is the comparison between HI‐6 and pralidoxime (2‐PAM), a smaller oxime previously studied in our research group. It is shown that conformation minima for the protonated E isomer do not depend on the size of the side chain; on the other hand, this effect has a pronounced influence on the protonated Z isomer. For the unprotonated isomers, other effects, such as electrostatic interactions and resonance, should be taken into account in their conformational analysis. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 相似文献
19.
20.
ZHAO Hongmei SUN Chengke ZHANG Rongchang XI Hongmin & LI Zonghe . Department of Chemistry Beijing Normal University Beijing China . The Laboratory of Molecular Reaction Dynamics Institute of Chemistry Chinese Academy of Sciences Beijing China . Department of Chemistry Beihua University Jilin China . Department of Chemistry Qujing Normal University Yunnan China 《中国科学B辑(英文版)》2005,48(1)
The global environment pollution includes pho-tochemical smog, acid rain and stratospheric ozonedepletion. The short-lived species/radicals in atmos-phere are closely related to these phenomena. Theshort-lived species/radicals bring the photochemicalsmog,… 相似文献