Comparison of HF,HF + MP2, LDA,BLYP, and B3LYP band structures of the homopolypeptides

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 VB_max 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     

Correlation corrected band structures of homopolypeptides v. B3LYP band structures of 19 homopolypeptides

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     

HCS自由基超精细结构的密度泛函理论计算

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．…     

Assessment of the OLYP and O3LYP density functionals for first-row transition metals

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.     

Enthalpies of formation from B3LYP calculations

We have calculated the geometries, energies, and normal vibrations of 845 compounds containing the elements H, C, N, O, F, Al, Si, P, S, and Cl using hybrid density functional theory in order to investigate the accuracy of atom-additive schemes for predicting enthalpies of formation at 298 K. The results give a more realistic estimate of the accuracy of density functional calculations than some overoptimistic earlier correlations. We have also calculated atom-additive schemes for the zero-point energies and enthalpic corrections to the energies. Remarkably, it is not important to include the vibrational or rotational contributions, which can be estimated well within a purely Born-Oppenheimer regression model.     

Accurate prediction of heats of formation by a combined method of B3LYP and neural network correction

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     

戊烯自由基阳离子的密度泛函理论研究

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.     

B3LYP calculations on bishomoaromaticity in substituted semibullvalenes*

B3LYP/6‐31G* calculations on the degenerate rearrangements of substituted semibullvalenes spuriously predict the relative enthalpies of the bishomoaromatic TSs to be lower than the experimental values. However, the calculations do make the useful and experimentally testable prediction that the two cyano and two phenyl substituents in 2,6‐dicyano‐4,8‐diphenylsemibullvalene ( 9d ) are more likely than four cyano substituents in 2,4,6,8‐tetracyanosemibullvalene ( 9f ) or the four phenyl substituents in 2,4,6,8‐tetraphenylsemibullvalene ( 9g ) to produce a semibullvalene that has a bishomoaromatic equilibrium geometry in the gas phase. The major reason for the surprising finding that 9d is more likely to be bishomoaromatic than 9g is shown to be steric interactions between the phenyl groups at C‐2 and C‐8 and at C‐4 and C‐6 in bishomoaromatic structure 10g . These interactions inhibit the conjugative stabilization of 10g ; but they are absent in bishomoaromatic structure 10d , where cyano groups replace the phenyl groups at C‐2 and C‐6 in 10g . © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1565–1573, 2001     

Geometry optimization of the cytosine molecules in a cytosine stack using the B3LYP crystal orbital method

The B3LYP DFT crystal orbital method was applied (with helical periodicity) to calculate the total energy per unit cell of a cytosine (C) molecule in a C stack. Applying afterwards the multidimensional metric method in its BFGS form, the geometry of a C molecule was optimized in the stack of DNA B (3.36 Å stacking distance, 36° rotation). For comparison, we optimized also the geometry of a C trimer and pentamer (in DNA B form) using the Gaussian 03 program for the B3LYP molecular calculation and the default method for the geometry optimization. The results of the two completely different calculations agree quite well, which supports our confidence in the results of our C stack calculation. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

C~3~6二聚体的结构和稳定性的理论研究

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。     

Novel H-bonded base dimers as repeat units for information-bearing self-associative duplexes: a B3LYP/6-31G* search

Density functional theory at the B3LYP/6-31G* level with counterpoise correction has been employed to study six sets of nitrogenous bases for the capacity of each to form H-bonded dimers restricted to a chosen pairing configuration. These results are augmented by MP2/6-311++G(d,p) single point calculations on the B3LYP/6-31G* optimized geometries. Each set has two bases, including substituted azoles, imidazoles, pyrimidines, and fused ring systems. This study aims to determine the suitability of each set to furnish H-bonded base pairs which may serve as repeat units for self-associative H-bonded macromolecular duplexes with the capacity to store and replicate information at the molecular level. Out of the various possibilities tested here, a set of two substituted pyrimidines best satisfies the prescribed criteria and may be put forward as a good candidate to yield isomorphic repeat units for designing such synthetic information-bearing macromolecular duplexes. The optimized configurations of these chosen base pairs as calculated at the B3LYP/6-31G* level compare well with those calculated at the B3LYP/6-31++G(d,p) and MP2/6-31G(d,p) levels, and indicate that isomorphism of the two base pairs is independent of method used. Assuming a one-to-one correspondence for encoding information in the macromolecule, such a set of two bases can allow the macromolecule to encode up to 8 types of encrypted species.     

已烯自由基阳离子的密度泛函理论研究

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。     

含能材料六硝基六氮杂异伍兹烷分子的B3LYP研究

在B3LYP/6-31G^**水平上对六硝基六氮杂异伍兹烷(CL-20)分子进行结构优化、集居数分析、自然键轨道和振动频率计算,得到与实验值相符的稳定构型.根据计算结果,讨论了键特性对分子性质的影响.     

Synthesis,characterization, structures,and DFT study of zinc(II) complexes with tributylphosphine chalcogenides

Four new zinc(II) complexes of the type [ZnCl₂(n-Bu₃PE)₂] (E=O (1), S (2), Se (3), or Te (4)) have been synthesized from zinc(II) chloride and the ligands n-Bu₃PE giving yields of 56–88%. The adducts were characterized by multinuclear (³¹P, ¹³C, and ⁷⁷Se) NMR, conductivity, IR spectroscopy and by X-ray analyses. Zinc complexes 1–4 are compriseS of two ligands coordinated to the metal center in a distorted tetrahedral arrangement. The P=E bond lengths of 1.497(7) (E=O), 2.000(4) (E=S), and 2.178(2) Å (E=Se) in these complexes are slightly elongated compared to those in the free ligand. In addition, a DFT/B3LYP theoretical study on the geometry optimization of the title ligands and their zinc complexes has been carried out in order to support and complement the experimental data and to further investigate the nature of the chalcogenide-metal interaction. The results show good agreement between the experimental and theoretical data.     

DFT方法理论研究星际分子C3S+结构和光谱

在B3LYP／6—31lG(d)水平上对可能的星际分子C3S^ 的各种异构体进行了理论计算研究，得到其几何构型、红外光谱和精确能量以利于实验室和星际观测，讨论了其星际含义，并与其中性分子C3S做了比较．结果表明：C3S^ 有3个稳定的异构体，包括线形、三元环和四元环几何构型．按热力学稳定的异构体依次是直线型具有C∞v对称性的CCCS^ (1)，其次是具有CC桥键四元环构型的cC3S^ (2)，能量最高是三元环构型具有CC环外键的C—cCCS^ (3)。     

A DFT Study for NH3 Adsorption on the GaN （0001） Surface

1 INTRODUCTION Recently, the reaction of NH3 with III-V com- pounds[1～5] has attracted much attention, especially for the wurtzite GaN, since NH3 is the predominant raw stuff for growing crystalline GaN by both of the most important growth techniques[6～9], i.e., organo- metallic chemical vapor deposition (OMCVD) and molecular-beam epitaxy (MBE). Experimentally, Shekhar et al.[2] reported the chemisorption and reaction of hydrogen and ammonia on the single- crystalline GaN (0001…     

Theoretical study of spectroscopic constants and molecular properties of diatomic anions using B3LYP method

Structure, spectroscopic constants and molecular properties of selected diatomic anions in their ground states have been studied in detail using HF/DF B3LYP method. The consistency of the calculated values of spectroscopic constants and molecular properties has been tested using four basis sets with improved quality. The spectroscopic constants and molecular properties of these diatomic ions agree well with the experimental and theoretical values wherever available. Most of the spectroscopic constants and molecular properties of these ions, in particular the spectroscopic constants of SiO⁻, CS⁻ and the molecular properties of SiN⁻, CP⁻, SiO⁻ are first reported.     

Application of the DFT Theory to Study Cobalamin Complexes

The aim of present study is to select the best methodology in the frame of the Density Functional Theory (DFT), which may be employed to study the cobalamin complexes. Our discussion is limited to two approaches, one in which hybrid B3LYP and UB3LYP functionals are used, and the second in which geometry parameters are calculated within LDA-VWN functional, and energies of the investigated systems are computed within RPBE functional. Results of performed calculations show that both methodologies can be successfully applied to study cobalamin derivatives. Probably because of the small ligand binding energies in the studied complexes, the B3LYP and UB3LYP functionals may be used only to predict the pattern of changes in the binding energies. The use of the RPBE functional, originally parameterized to reproduce in a proper way the chemisorption energies of the small molecules on the metallic surfaces, allows to improve their values so as they fit into experimental data. Geometry parameters of the investigated complexes computed within both approaches are in good agreement with the experimental values. Interatomic distances are a little overestimated while calculated within both hybrid functionals, what is in contrast to VWN functional results. The latter, in general, gives shorter distances as observed experimentally.     

DFT conformational studies of the HI‐6 molecule

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     

trans-1,2-Dicyano-cyclopropane and other cyano-cyclopropane derivatives

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.