An efficient method for calculating atomic charges of peptides and proteins from electronic populations

An efficient method is presented to calculate atomic charges of peptides and proteins derived from Mulliken electronic populations for terminally blocked amino acids (Ac-X-NHMe, X = any neutral or charged residue) calculated at the B3LYP/6-31G(d,p)//HF/6-31G(d,p) level of theory. This electronic population-derived atomic charges (EPAC) method is based on the geometry-dependent atomic charge (GDAC) method proposed by Cho et al. (J. Phys. Chem. B 2001, 105, 3624), in which atomic charges are calculated by using the partial equalization of atomic electronegativities with electronegativity parameters and damping factors given by interatomic distances between covalently bonded atoms in a molecule. The overall mean absolute difference (mad) and root-mean-square deviation (rmsd) between dipole moments micro(EPAC) and micro(B3LYP), obtained from EPAC charges and from B3LYP/6-31G(d,p) level calculations, respectively, for Ac-X-NHMe are estimated to be 0.38 and 0.59 D, respectively, for 26 representative conformations in the training set, and 0.54 and 0.79 D, respectively, for 172 representative conformations not used for parametrization. For Ac-(Ala)(n)-NHMe (n = 2-6), the EPAC method reasonably predicts the increase of the dipole moment with increase of the chain length, although the deviations from the micro(B3LYP) values are somewhat larger. For Ac-Ala-NHMe and Ac-(Ala)(3)-NHMe, the EPAC charge for a specific type of atom does not depend on its position in the sequence or on the length of the sequence. In addition, charge neutrality holds for any Ala residue of these two peptides. Thus, these results suggest that the EPAC charges derived from B3LYP/6-31G(d,p) Mulliken populations can be used reliably for conformational analysis of peptides and proteins.     

Quantum vs. classical models of the nitro group for proton chemical shift calculations and conformational analysis

A model based on classical concepts is derived to describe the effect of the nitro group on proton chemical shifts. The calculated chemical shifts are then compared to ab initio (GIAO) calculated chemical shifts. The accuracy of the two models is assessed using proton chemical shifts of a set of rigid organic nitro compounds that are fully assigned in CDCl3 at 700 MHz. The two methods are then used to evaluate the accuracy of different popular post-SCF methods (B3LYP and MP2) and molecular mechanics methods (MMX and MMFF94) in calculating the molecular structure of a set of sterically crowded nitro aromatic compounds. Both models perform well on the rigid molecules used as a test set, although when using the GIAO method a general overestimation of the deshielding of protons near the nitro group is observed. The analysis of the sterically crowded molecules shows that the very popular B3LYP/6-31G(d,p) method produces very poor twist angles for these, and that using a larger basis set [6-311++G(2d,p)] gives much more reasonable results. The MP2 calculations, on the other hand, overestimate the twist angles, which for these compounds compensates for the deshielding effect generally observed for protons near electronegative atoms when using the GIAO method at the B3LYP/6-311++G(2d,p) level. The most accurate results are found when the structures are calculated using B3LYP/6-311++G(2d,p) level of theory, and the chemical shifts are calculated using the CHARGE program based on classical models.     

An ab initio (RHF) and DFT-B3LYP level spectroscopic studies of BrCCCN and the analysis of atomic polar tensors

Conventional ab initio (RHF) and DFT-B3LYP level calculations in conjunction with a variety of basis sets have been used to investigate the variations in the bond lengths, dipole moment, rotational constant, quadruple coupling constants, infrared frequencies, IR intensities and rotational invariants of BrCCCN. Satisfactory agreements between the B3LYP and experimental values were found for bond lengths, rotational constant, dipole moment and all other parameters. All the calculated bond lengths are in good agreement with each other for a given method having the average standard deviations varying between ±0.005 Å at the B3LYP level. Harmonic vibrational frequencies obtained from the B3LYP calculations show good agreement with the available experimental data. The global atomic polar tensor charges, used for interpreting the IR intensities, of all the atoms of BrCCCN have been calculated at the RHF and B3LYP levels in conjunction with the 6-311g(d) and 6-311++g(d,p) basis sets. Linear regression analysis between calculated and experimental infrared frequencies as well as between IR intensities in a series of 15 similar type of nitrile compounds have been achieved at the B3LYP/6-311++g(d,p) level and gives linear regression coefficients 0.983 and 0.970 respectively. Finally, a number of linear relations were found between r(CN) bond lengths and GAPT charges, and GAPT charges on CHELPG and MK charges at the nitrogen atom for these molecules and proved to be producing satisfactory results at the B3LYP/6-311++g(d,p) level of calculations.     

NMR spectra, GIAO and charge density calculations of five-membered aromatic heterocycles

The B3LYP/6-31+G(d) molecular geometry optimized structures of 17 five-membered heterocycles were employed together with the gauge including atomic orbitals (GIAO) density functional theory (DFT) method at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p) and B3LYP/6-311+G(2d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants. The method of geometry optimization for pyrrole (1), N-methylpyrrole (2) and thiophene (7) using the larger 6-311++G(d,p) basis sets at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,p) and B3LYP/cc-pVTZ levels of theory gave little difference between calculated and experimental values of coupling constants. In general, the (1)H and 13C chemical shifts for all compounds are in good agreement with theoretical calculations using the smaller 6-31 basis set. The values of nJHH(n=3, 4, 5) and rmnJ(CH)(n=1, 2, 3, 4) were predicted well using the larger 6-31+G(d,p) and 6-311++G(d,p) basis sets and at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,2p) levels of theory. The computed atomic charges [Mülliken; Natural Bond Orbital Analysis (NBO); Merz-Kollman (MK); CHELP and CHELPG] for the B3LYP/6-311++G(d,p) geometry optimized structures of 1-17 were used to explore correlations with the experimental proton and carbon chemical shifts.     

Theoretical investigation on multinuclear NMR chemical shifts of some tris(trifluoromethyl)boron complexes

Tris(trifluoromethyl)boron complexes have unusual properties and may find applications in many fields of chemistry, biology, and physics. To gain insight into their NMR properties, the isotropic ¹¹B, ¹³C, and ¹⁹F NMR chemical shifts of a series of tris(trifluoromethyl)boron complexes were systematically studied using the gauge‐included atomic orbitals (GIAO) method at the levels of B3LYP/6‐31 + G(d,p)//B3LYP/6‐31G* and B3LYP/6‐311 + G(d,p)//B3LYP/6‐311 + G(d,p). Solvent effects were taken into account by polarizable continuum models (PCM). The calculated results were compared with the experimental values. The reason that the structurally inequivalent fluorine atoms in a specific species give a same chemical shift in experimental measurements is attributed to the fast rotation of CF₃ group around the B? C(F₃) bond because of the low energy barrier. The calculated ¹¹B, ¹³C(F₃), and ¹⁹F chemical shifts are in good agreement with the experimental measurements, while the deviations of calculated ¹³C(X, X = O, N) chemical shifts are slightly large. For the latter, the average absolute deviations of the results from B3LYP/6‐311 + G(d,p)//B3LYP/6‐311 + G(d,p) are smaller than those from B3LYP/6‐31 + G(d,p)//B3LYP/6‐31G*, and the inclusion of PCM reduces the deviation values. The calculated ¹⁹F and ¹¹B chemical shieldings of (CF₃)₃BCO are greatly dependent on the optimized structures, while the influence of structural parameters on the calculated ¹³C chemical shieldings is minor. Copyright © 2009 John Wiley & Sons, Ltd.     

CH_2CO+CH_2的多通道反应的理论研究

利用密度泛函(DFT)和自然键轨道理论(NBO)及高级电子耦合簇[CCSD(T)]和电子密度拓扑(AIM)方法,对单重态和三重态CH2与CH2CO反应的微观机理进行了研究.在B3LYP/6-311+G(d,p)水平上优化了反应通道各驻点的几何构型.在CCSD(T)/6-311+G(d,p)水平上计算了各物种的单点能量,并对总能量进行了校正.计算表明,单重态CH2与CH2CO的C-H键可发生插入反应,与C=C、C=O可发生加成反应,存在三条反应通道,产物为CO和C2H4,从能量变化和反应速控步骤能垒两方面考虑,反应II更容易发生.对反应通道中的关键点进行了自然键轨道及电子密度拓扑分析.三重态CH2与CH2CO的反应存在三条反应通道,一条是与C-H键的插入反应,另一条是三重态CH2与C=C发生加成反应,产物为CO和三重态C2H4,通道II势垒较低,更容易发生.最后一条涉及双自由基的反应活化能最大,最难发生.     

Spectroscopic characterization and single molecule structures of N,N-bis-(3-phthalimidopropyl)-N-(2-hydroxyethyl)-N-propylammonium salts and their hydrates

N,N-Bis-(3-phthalimidopropyl)-N-(2-hydroxyethyl)-N-propylammonium salts and their hydrates have been characterized by FTIR, Raman and NMR spectroscopy. Also B3LYP and PM5 calculations have been carried out. The optimized bond lengths, bond angles and torsion angles calculated by B3LYP/6-31G(d,p) approach have been compared with the spectroscopic data. The screening constants for ¹³C and ¹H atoms have been calculated by the GIAO/B3LYP/6-31G(d,p) approach and analyzed. Linear correlations between the experimental ¹H and ¹³C chemical shifts and the computed screening constants confirm the optimized geometry.     

Accurate Prediction of Absorption Spectral Shifts of Proteorhodopsin Using a Fragment-Based Quantum Mechanical Method

Many experiments have been carried out to display different colors of Proteorhodopsin (PR) and its mutants, but the mechanism of color tuning of PR was not fully elucidated. In this study, we applied the Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps (EE-GMFCC) method to the prediction of excitation energies of PRs. Excitation energies of 10 variants of Blue Proteorhodopsin (BPR-PR105Q) in residue 105GLN were calculated with the EE-GMFCC method at the TD-B3LYP/6-31G* level. The calculated results show good correlation with the experimental values of absorption wavelengths, although the experimental wavelength range among these systems is less than 50 nm. The ensemble-averaged electric fields along the polyene chain of retinal correlated well with EE-GMFCC calculated excitation energies for these 10 PRs, suggesting that electrostatic interactions from nearby residues are responsible for the color tuning. We also utilized the GMFCC method to decompose the excitation energy contribution per residue surrounding the chromophore. Our results show that residues ASP97 and ASP227 have the largest contribution to the absorption spectral shift of PR among the nearby residues of retinal. This work demonstrates that the EE-GMFCC method can be applied to accurately predict the absorption spectral shifts for biomacromolecules.     

Prediction of the 13C NMR Chemical Shifts of Fluorenone Analogues by the GIAO Method

After the geometry optimization at B3LYP/6-31+G(d,p) level,the NMR calcula-tions of a series of fluorenone analogues have been carried out by GIAO method at HF/6-31+G(d) level and B3LYP/6-311G+(2d,p) level,respectively.The 13C NMR chemical shifts calculated at HF/6-31+G(d) level show better agreement with the observed values.By a series of linear correction equations (δpred=a + bδcalc),accurate prediction of 13C chemical shifts was achieved for the new fluorenone compound.The linear correlation of δpred with δexptl is excellent,and the square of correlation coefficient,r2,is up to 0.994.The maximum absolute difference between δpred and δexptl,Δδ,is 4.6 ppm,and the root-mean-square error between δpred and δexptl is only 2.6 ppm.     

2-丁基-四氢噻吩亚砜13C-NMR的理论研究

在RHF/6-31G和B3LYP/6-31G水平上对顺式(Cis-)与反式(Trans-)2-丁基-四氢噻吩亚砜(BTHTO)进行几何优化,应用规范不变原子轨道法(GIAO)在6-31G、6-31+G、6-31++G和6-31+G(2d,p)水平上计算了Cis-和Trans-BTHTO的13C-NMR,对13C-NMR谱进行了归属。结果表明,BTHTO噻吩五元环的稳定构象呈半椅式,Cis-和Trans-BTHTO中与硫原子直接碳原子13C-NMR的显著差异主要是由于空间构型不同引起分子的静电势场对相应碳原子的屏蔽作用不同所致。     

Experimental (FT-IR and FT-Raman), electronic structure and DFT studies on 1-methoxynaphthalene

In this work, FT-IR and FT-Raman spectra of 1-methoxynapthalene (C(11)H(10)O) have been reported in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. Density functional method (DFT) has been used to calculate the optimized geometrical parameters, atomic charges, vibrational wavenumbers and intensity of the vibrational bands. The vibrational frequencies have been calculated and scaled values are compared with experimental FT-IR and FT-Raman spectra. The structure optimizations and normal coordinate force field calculations are based on density functional theory (DFT) method with B3LYP/3-21G, B3LYP/6-31G, B3LYP/6-31G(d,p) and B3LYP/6-311++G(d,p) basis sets. The complete vibrational assignments of wavenumbers are made on the basis of potential energy distribution (PED). The optimized geometric parameters are compared with experimental values of naphthoic acid. The results of the calculation shows excellent agreement between experimental and calculated frequencies in B3LYP/6-311++G(d,p) basis set. The effects due to the substitutions of methyl group and carbon-oxygen bond are also investigated. A study on the electronic properties, such as excitation energies and wavelengths, were performed by time-dependent DFT (TD-DFT) approach. HOMO and LUMO energies are calculated that these energies show charge transfer occurs within the molecule.     

NMR spectra of free-base porphine, porphyrazine, phthalocyanine and naphthalocyanine as well as their metal complexes: density functional calculations

Nuclear magnetic shielding tensors of porphine have been calculated at density functional B3LYP and PBE level using the gauge independent atomic orbital (GIAO) method. The geometries used were optimized using the 6-31G(d) basis set and the NMR calculations were performed using 6-31G(d) and 6-311G(d,p) basis sets, respectively. The calculated NMR shielding tensors and chemical shifts of porphine are compared with previous calculations as well as experimental data and satisfying results are obtained. Further NMR calculations are extended to metal-free and metallo-porphyrazine, -phthalocyanine, and -naphthalocyanine for the first time and the results are compared with experimental data available. The chemical shifts of the atoms in these compounds are assigned according to the experimental data available.     

Theoretical binding affinities and spectroscopy of complexes formed by cyclobis(paraquat-<Emphasis Type="Italic">p</Emphasis>-anthrancene) with some pharmaceutical molecules

Theoretical investigation on the stabilities and spectroscopic properties of the complexes formed by cyciobis(paraquat-p-anthracene) with pharmaceutical molecules were performed using the semi-empirical PM3 and B3LYP/3-21G methods. Based on the B3LYP/3-21G optimized geometries, the energies of the complexes were calculated at B3LYP/6-31G(d) level. The binding energies of the complexes were computed after the correction of basis set superposition error (BSSE). The energy gaps of the complexes are decreased due to the formation of the hydrogen bonds. The stretching vibrations of the C-H bonds adjacent to the hydrogen bonds in the IR spectra of the complexes calculated with PM3 method are red-shifted compared with those of the host. The chemical shifts of α-C and β-C atoms in the complexes calculated at B3LYP/3-21G level are shifted downfield due to the formation of the hydrogen bonds and the electron-withdrawing effect of the nitrogen atoms. The aromaticities of the complexes are improved because of the enlargement of the conjugation system and the overlap of electron cloud based on the nuclear independent chemical shifts (NICS) calculated at B3LYP/3-21G level.     

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.     

Ab initio Study on Structures and Isomerization of Magnesium Fluorosilylenoid H2SiFMgF

The structures and isomerization of magnesium fluorosilylenoid H2SiFMgF were investigated by ab initio molecular orbital theory. Four equilibrium structures and three isomeric transition states were located and fully optimized at the B3LYP/6-31G(d,p) and G3MP2B3 levels, respectively. Based on the B3LYP/6-31G(d,p) optimized geometries, harmonic frequencies of various structures were obtained and 29Si chemical shifts were calculated. The solvent effects were investigated by means of the polarizable continuum model using THF as a solvent at B3LYP/6-31G(d,p) level. Isomerization paths for isomers were confirmed by intrinsic reaction coordinate calculations. The calculated results show that tetrahedral structure has the lowest energy and is the most stable; tetrahedral, three-membered ring, and p-complex structures are suggested to be the experimentally detectable ones; and σ-complex structure has the highest energy and will not exist.     

DFT study of conjugational electronic structures of aminoalkyl end-capped oligothiophenes up to octamers

The molecular geometries and electronic properties of a series of bis(aminoalkyl) end-capped oligothiophenes (BRnTs) were investigated by means of the density functional theory (DFT). The calculations were performed on dimers up to octamers in the neutral and ionic species using the B3LYP/6-31G(d,p) level of theory. The results obtained show that the conjugated systems in the p- and n-doped oligomers had more aromaticity, with expanded and planar chains. The calculated energy gap values between the frontier molecular orbitals for the end-capped oligomers were larger than those for the unsubstituted oligomers, in which with increase in the oligomer chain length, the conduction band gap decreased. The calculated first excitation energies of BRnTs at the TD-B3LYP/6-31G(d,p) level indicated that both doped oligomers (p- and n-type) had lower excitation energies than the neutral states, and that they displayed red shifts in their absorption spectra. Moreover, the results obtained for the natural bond orbital (NBO) analysis showed that closing the end-side oligothiophene chains with the aminoalkyl groups eased the hole or electron transfer, owning to better charge delocalization through the backbone structures of BRnTs.     

Ab initio- and density-functional studies of conformational behaviour of N-formylmethionine in gaseous phase

The current work is a study of the conformational space of the non-ionic N-formylmethionine molecule around its seven structurally significant internal backbone torsional angles at B3LYP/6-31++G(d,p) levels of theory in the gaseous phase. The potential energy surface exploration reveals that a total of 432 different conformers would result if all the possible combinations of the internal rotations were to be considered. A set of twelve conformers of the N-formylmethionine molecule are then further analysed in terms of their relative stabilities, theoretically predicted harmonic vibrational frequencies, HOMO-LUMO energy gaps, ESP charges, rotational constants and dipole moments calculated using MP2/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels. The calculated relative energy-range of the conformers at the MP2 level is 11.08 kcal mol^?1 (1 kcal = 4.1868 kJ), whereas the same obtained at the B3LYP level is 10.02 kcal mol^?1. The results of this study provide a good account of the role of four types of intramolecular H-bonds, namely O…H—O, O…H—N, O…H—C and N…H—C, in influencing the energies of the conformers as well as their conformational and vibrational spectroscopic aspects. The relative stability order of the conformers appears to depend on the level of theory used while the vibrational frequencies calculated at the B3LYP level are in better agreement with the experimental values.     

类硅烯H2C＝SiLiBr与RH (R＝F, OH, NH2)的插入反应

采用DFT B3LYP和QCISD方法研究了类硅烯H2C＝SiLiBr与RH (R＝F, OH, NH2)的插入反应. 在B3LYP/6- 311＋G(d,p)水平上优化了反应势能面上的驻点构型. 结果表明, H2C＝SiLiBr与HF, H2O或NH3发生插入反应的机理相同. QCISD/6-311＋＋G(d,p)//B3LYP/6-311＋G(d,p)计算的三个反应的势垒分别为148.62, 164.42和165.07 kJ&#8226;mol－1, 反应热分别为－69.63, －43.02和－28.27 kJ&#8226;mol－1. 相同条件下发生插入反应时, 反应活性都是H—F＞H—OH＞H—NH2.     

Density functional theory calculation of 13C NMR shifts of diazaphenanthrene alkaloids: reinvestigation of the structure of samoquasine A

The (13)C NMR shifts of 48 diazaphenanthrene-type alkaloids have been calculated at the B3LYP/6-311+G(2d,p) level of theory. The results support the structural reassignment of samoquasine A as 2.     

A theoretical study of inversion barriers and NMR chemical shifts of 3-pyrazolines (2,3-dihydro-1H-pyrazoles)

A rather neglected family of heterocyclic compounds, the 3-pyrazolines or 2,3-dihydro-1H-pyrazoles, has been studied theoretically at the B3LYP/6–311++G(d,p) level to obtain geometries and energies and at the GIAO/B3LYP/6–311++G(d,p) level for NMR chemical shifts. The calculated barriers of inversion of the N-substituents reproduce adequately the scarce experimental data. The calculated ¹H and ¹³C chemical shifts are consistent with those reported in the literature. A combination of both results, geometries, and ¹³C chemical shifts, shed light on the conformation of N-phenyl groups.