Second order Møller-Plesset perturbation theory based upon the fragment molecular orbital method

The fragment molecular orbital (FMO) method was combined with the second order M?ller-Plesset (MP2) perturbation theory. The accuracy of the method using the 6-31G(*) basis set was tested on (H(2)O)(n), n=16,32,64; alpha-helices and beta-strands of alanine n-mers, n=10,20,40; as well as on (H(2)O)(n), n=16,32,64 using the 6-31 + + G(**) basis set. Relative to the regular MP2 results that could be afforded, the FMO2-MP2 error in the correlation energy did not exceed 0.003 a.u., the error in the correlation energy gradient did not exceed 0.000 05 a.u./bohr and the error in the correlation contribution to dipole moment did not exceed 0.03 debye. An approximation reducing computational load based on fragment separation was introduced and tested. The FMO2-MP2 method demonstrated nearly linear scaling and drastically reduced the memory requirements of the regular MP2, making possible calculations with several thousands basis functions using small Pentium clusters. As an example, (H(2)O)(64) with the 6-31 + + G(**) basis set (1920 basis functions) can be run in 1 Gbyte RAM and it took 136 s on a 40-node Pentium4 cluster.     

离子簇合物HeN_2~+的电子光谱的从头算研究

本文报道了离子簇合物HeN2＋的电子光谱的从头算结果。在MCSCF／6－31G（d，p）水平上，对其基态进行了几何优化，用该构型．在SDC1／6－31（d，p）水平上计算了基态的总能量。用SDCI方法计算得到HeN2＋从基态到选择激发态的垂直跃迁能、振子强度、跃迁频率、辐射寿命以及Einstain系数。该结果可以较好的验证maier的实验。     

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.     

Infrared experimental and ab initio quantum mechanical studies of 2-mercaptopyrimidine tautomers

Results are presented from ab initio SCF(3-21G*) calculations for the geometries and vibrational spectra (wavenumbers and absolute intensifies) of the thiol and thione tautomers of 2-mercaptopyrimidine. The results of calculations are compared with available experimental data, particularly with the reported vibrational spectra of the molecule isolated in inert gas matrices (Ar, N₂) and in crystalline state. The calculations of the normal modes predicted the experimental spectrum close enough to allow reliable assignment of most of the bands. The thiol⇌⇌thione tautomerism of the molecule is discussed. Matrix isolated monomers were observed in the thiol form only. That agrees with the results of ab initio calculations of internal energies of the tautomers [SCF(6-31Gu*) + MBPT(2)(6-31G*) + vib(0)(3-21G*); at the SCF(3-21G*) geometries] which predict the energy of thiol form to be ≈33 kJ mol⁻¹ lower than that of thione form. In the crystalline state the hydrogen-bonded associations in the thione form dominate while in disordered amorphous layers, in matrices with a high guest-to-host ratio and in annealed matrices the associations both in thiol and thione form were observed.     

Characterization of hydrated Na+(phenol) and K+(phenol) complexes using infrared spectroscopy

Hydrated alkali metal ion-phenol complexes were studied to model these species in aqueous solution for M=Na and K. IR predissociation spectroscopy in the O-H stretch region was used to analyze the structures of M+(Phenol)(H2O)n cluster ions, for n = 1-4. The onset of hydrogen bonding was observed to occur at n=4. Ab initio calculations were used to qualitatively explore the types of hydrogen-bonded structures of the M+(Phenol)(H2O)4 isomers. By combining the ab initio calculations and IR spectra, several different structures were identified for each metal ion. In contrast to benzene, detailed in a previous study of Na+(Benzene)n(H2O)m [J. Chem. Phys. 110, 8429 (1999)], phenol is able to bind directly to Na+ even in the presence of four waters. This is likely the result of the sigma-type interaction between the phenol oxygen and the ion. With K+, the dominant isomers are those in which the phenol O-H group is involved in a hydrogen bond with the water molecules, while with Na+, the dominant isomers are those in which the phenol O-H group is free and the water molecules are hydrogen-bonded to each other. Spectra and ab initio calculations for the M+(Phenol)Ar cluster ions for M=Na and K are reported to characterize the free phenol O-H stretch in the M+(Phenol) complex. While pi-type configurations were observed for binary M+(Phenol) complexes, sigma-type configurations appear to dominate the hydrated cluster ions.     

Anisotropic and hydrogen bonding effects in phenylglyoxamides and mandelamides: theoretical and NMR conformational evaluation

Interesting anisotropic effects were observed for phenylglyoxamides and their respective mandelamides. Such effects were observed in experimental (1)H and (13)C NMR (in CDCl(3), CD(3)OD, and DMSO-d(6) solvents) and in some cases with good correlation to theoretical (1)H and (13)C NMR DFT-GIAO (B3LYP/6-311++G**//B3LYP/6-31G*) calculations. A systematic conformational analysis of these compounds was performed in a two-step methodology, using PM3 and DFT (B3LYP/6-31G*) calculations; with good accomplishment and computational time economy. It was observed that intramolecular hydrogen bonding plays a significant role in the conformation of such compounds. Finally, a geminal nonequivalence of an N-CH(2) moiety, in one of the alkyl side chain (R1 = R2), was found for the tertiary mandelamides studied.     

含轴向咪唑配体的手性SalenCo(III)配合物ECD谱的理论解析

用密度泛函理论(DFT)方法, 在B3LYP和混合基组(C, H原子用6-31G^*; Co, N, O用6-311+G(2d,p))水平上, 对含轴向配体的三种Co(III)席夫碱配合物[Co(MeO-salen)(Im)₂]⁺、[Co(MeO-salen)(2-MeIm)₂]⁺和[Co(MeO-salen)(MeIm)₂]⁺ (Im=咪唑, MeIm=1-甲基咪唑, 2-MeIm=2-甲基咪唑, MeO-salenH₂=salen型席夫碱, 即(R,R)-N,N′-双(5-甲氧基亚水杨基)-1,2-二亚胺基环己烷)在二氯甲烷溶液中的基态结构进行了优化, 并用含时密度泛函理论(TDDFT)方法, 在相同泛函和基组水平上计算了其激发能、振子强度和旋转强度. 这些计算中均用极化连续介质模型(PCM)考虑了溶剂效应. 计算的电子圆二色(ECD)谱与实验谱吻合较好. 通过对有关跃迁性质的分析, 对实验电子圆二色光谱进行了解析与指认. 结果表明, 长波区的第一个圆二色(CD)吸收带主要是由π→d荷移跃迁(LMCT)引起的, 而不是通常认为的d→d跃迁. 轴向配体的加入对配合物前两个CD吸收带的符号没有影响, 但会影响带形和强度. 手性salen配合物的绝对构型为λ(RR)时, 第一个CD吸收带为正, 第二个为负. 这些结论对于深入理解该类配合物的电子结构和手征光学性质具有重要的科学意义.     

Quantum chemical calculations based on ONIOM and the DFT methods in the inclusion complex: doxycycline/2-O-Me-β-cyclodextrin

A computational study of inclusion complexes of 2-methyl-βCD with Doxycycline tautomeric (enol and keto form) has been performed with several combinations of ONIOM hybrid calculations. The reliability of the ONIOM2 calculations at the integrated level, ONIOM2 (M05-2X/6-31G(d): M05-2X/3-21G*), ONIOM2 (M05-2X/6-31G(d):HF/3-21G*), ONIOM2 (B3LYP/6-31G(d):HF/3-21G*), ONIOM2 (B3LYP/6-31G(d):B3LYP/3-21G*) and ONIOM2 (B3PW91/6-31G(d):B3PW91/3-21G*) was examined. Their complexation, binding, deformation and stabilization energies, and geometrical data were compared with those of the target geometry structure optimized at the M05-2X/6-31G(d) level of theory. Mixed combinations ONIOM2 (M05-2X 6-31G(d):HF 3-21G*) and ONIOM2 (B3LYP 6-31G(d):HF 3-21G*) reproduces nearly the target geometry structure and provides realistic energetic results at a relatively low computational cost.     

Experimental and theoretical studies of sodium cation complexes of the deamidation and dehydration products of asparagine, glutamine, aspartic acid, and glutamic acid

The deamidation and dehydration products of Na+(L), where L = asparagine (Asn), glutamine (Gln), aspartic acid (Asp), and glutamic acid (Glu), are examined in detail utilizing collision-induced dissociation (CID) with Xe in a guided ion beam tandem mass spectrometer (GIBMS). Results establish that the Na+(L) complexes decompose upon formation in our dc discharge/flow tube ion source to form a bis-ligand complex, Na+(L-HX)(HX), composed of a sodium cation, the (L-HX) decomposition product, and HX, where HX = NH3 for the amides and H2O for the acids. Analysis of the energy-dependent CID cross sections for the Na+(L-HX)(HX) complexes provides unambiguous identification of the (L-HX) fragmentation products as 3-amino succinic anhydride (a-SA) for Asx and oxo-proline (O-Pro) for Glx. Furthermore, these experiments establish the 0 K sodium cation affinities for these five-membered ring decomposition products and the H2O and NH3 binding affinities of the Na+(a-SA) and Na+(O-Pro) complexes after accounting for unimolecular decay rates, the internal energy of reactant ions, and multiple ion-molecule collisions. Quantum chemical calculations are determined for a number of geometric conformations of all reaction species as well as a number of candidate species for (L-HX) at the B3LYP/6-311+G(d,p) level with single-point energies calculated at MP2(full), B3LYP, and B3P86 levels using a 6-311+G(2d,2p) basis set. This coordinated examination of both the experimental work and quantum chemical calculations allows for a complete characterization of the products of deamidation and dehydration of Asx and Glx, as well as the details of Na+, H2O, and NH3 binding to the decomposition species.     

Divide-and-conquer local correlation approach to the correlation energy of large molecules

A divide-and-conquer local correlation approach for correlation energy calculations on large molecules is proposed for any post-Hartree-Fock correlation method. The main idea of this approach is to decompose a large system into various fragments capped by their local environments. The total correlation energy of the whole system can be approximately obtained as the summation of correlation energies from all capped fragments, from which correlation energies from all adjacent caps are removed. This approach computationally achieves linear scaling even for medium-sized systems. Our test calculations for a wide range of molecules using the 6-31G or 6-31G( * *) basis set demonstrate that this simple approach recovers more than 99.0% of the conventional second-order Moller-Plesset perturbation theory and coupled cluster with single and double excitations correlation energies.     

Proton affinities of molecules containing nitrogen and oxygen: comparing ab initio and semiempirical results to experiments

We report a comparison of theoretical and experimental proton affinities at nitrogen and oxygen sites within a series of small molecules. The calculated proton affinities are determined using the semiempirical methods AM 1, MNDO , and PM 3; the ab initio Hartree–Fock method at the following basis levels: 3-21G //3-21G , 3-21+G //3-21G , 6-31G *//6-31G *, and 6-31+G (d, p)//6-31G *; and Møller–Plesset perturbation calculations: MP 2/6-31G *//6-31G *, MP 3/6-31G *//6-31G *, MP 2/6-31G +(d, p)//6-31G *, MP 3/6-31G +(d, p)//6-31G *, and MP 4(SDTQ )/6-31G +G (d, p)//6-31G *. The semiempirical methods have more nonsystematic scatter from the experimental values, compared to even the minimal 3-21G level ab initio calculations. The thermodynamically corrected 6-31G *//6-31G * proton affinities provide acceptable results compared to experiment, and we see no significant improvement over 6-31G *//6-31G * in the proton affinities with any of the higher-level calculations. © 1992 John Wiley & Sons, Inc.     

Coordination of methanol clusters to benzene: a computational study

Benzene-methanol cluster structures were investigated with theoretical chemistry methods to describe the microsolvation of benzene and the benzene-methanol azeotrope. Benzene-methanol (MeOH) clusters containing up to six methanol molecules have been calculated by ab initio [MP2/6-311++G(d,p)//MP2/6-31+G(d,p) + BSSE correction] method. The BSSE was found quite large with this basis set, hence, different extrapolation schemes in combination with the aug-cc-pVxZ basis sets have been used to estimate the complete basis set limit of the MP2 interaction energy [ΔE(MP2/CBS)]. For smaller clusters, n ≤ 3, DFT procedures (DFTB+, MPWB1K, M06-2X) have also been applied. Geometries obtained for these clusters by M06-2X and MP2 calculations are quite similar. Based on the MP2/CBS results, the most stable C(6)H(6)(MeOH)(3) cluster is characterized by a hydrogen bonded MeOH trimer chain interacting with benzene via π···H-O and O···H-C(benzene) hydrogen bonds. Larger benzene-MeOH clusters with n ≥ 4 consist of cyclic (MeOH)(n) subclusters interacting with benzene by dispersive forces, to be denoted by C(6)H(6) + (MeOH)(n). Interaction energies and cooperativity effects are discussed in comparison with methanol clusters. Besides MP2/CBS calculations, for selected larger clusters the M06-2X/6-311++G(d,p)//M06-2X/6-31+G(d,p) procedure including the BSSE correction was also used. Interaction energies obtained thereby are usually close to the MP2/CBS limit. To model the benzene-MeOH azeotrope, several structures for (C(6)H(6))(2)(MeOH)(3) clusters have been calculated. The most stable structures contain a tilted T-shaped benzene dimer interacting by π···H-O and O···H-C (benzene) hydrogen bonds with a (MeOH)(3) chain. A slightly less negative interaction energy results for a parallel displaced benzene sandwich dimer with a (MeOH)(3) chain atop of one of the benzene molecules.     

Thermochemical stabilities and structures of the cluster ions OCS+, S2+, H+(OCS), and C2H5+ with OCS molecules in the gas phase

The gas-phase clustering reactions of OCS+, S2+, H+(OCS), and C2H5+ ions with carbonyl sulfide (OCS) molecules were studied using a pulsed electron-beam high-pressure mass spectrometer and applying density functional theory (DFT) calculations. In the cluster ions OCS+(OCS)(n) and H+(OCS)(OCS)(n), a moderately strong, here referred to as "semi-covalent", bond was formed with n = 1. However, the nature of bonding changed from semi-covalent to electrostatic with n = 1 --> 2. The bond energy of S2(+)(OCS) was determined experimentally to be 12.9 +/- 1 kcal/mol, which is significantly smaller than that of the isovalent S2(+)(CS2) complex (30.9 +/- 1.5 kcal/mol). DFT based calculations predicted the presence of several isomeric structures for H+(OCS)(OCS)(n) complexes. The bond energies in the C2H5+(OCS)(n) clusters showed an irregular decrease for n = 1 --> 2 and 7 --> 8. The nonclassical bridge structure for the free C2H5+ isomerized to form a semi-covalent bond with one OCS ligand, [H3CCH2...SCO]+, i.e., reverted to classical structure. However, the nonclassical bridge structure of C2H5+ was preserved in the cluster ions C2H5+(OCS)(n) below 140 K attributable to the lack of thermal energy for the isomerization. DFT calculations revealed that stability orders of the geometric isomers of H+(OCS)(OCS)(n) and C2H5+(OCS)(n) changed with increasing n values.     

Experimental and DFT studies of ethyl N′-3-(1H-imidazol-1-yl) propylcarbamoyl benzohydrazonate monohydrate

The Imidazole compound, Ethyl N′-3-(1H-imidazol-1-yl) propylcarbamoyl benzohydrazonate monohydrate, has been synthesized and characterized by IR, NMR, electronic spectroscopy, and X-ray single-crystal determination. Molecular geometry from X-ray experiment of the title compound in the ground state has been compared using the density functional method (B3LYP) with 6-31G+(d) basis set. To determine conformational flexibility, molecular energy profile of the title compound was obtained by DFT calculations with respect to two selected degrees of torsional freedom, which were varied from −180° to +180° in steps of 10°. Besides, molecular electrostatic potential (MEP), natural bond orbitals (NBO), frontier molecular orbitals (FMO), and thermodynamic properties were performed at B3LYP/6-31G+(d) level of theory.     

Ab initio studies on Al(+)(H(2)O)(n), HAlOH(+)(H(2)O)(n-1), and the size-dependent H(2) elimination reaction

We report computational studies on Al(+)(H(2)O)(n), and HAlOH(+)(H(2)O)(n-1), n = 6-14, by the density functional theory based ab initio molecular dynamics method, employing a planewave basis set with pseudopotentials, and also by conventional methods with Gaussian basis sets. The mechanism for the intracluster H(2) elimination reaction is explored. First, a new size-dependent insertion reaction for the transformation of Al(+)(H(2)O)(n), into HAlOH(+)(H(2)O)(n-1) is discovered for n > or = 8. This is because of the presence of a fairly stable six-water-ring structure in Al(+)(H(2)O)(n) with 12 members, including the Al(+). This structure promotes acidic dissociation and, for n > or = 8, leads to the insertion reaction. Gaussian based BPW91 and MP2 calculations with 6-31G* and 6-31G** basis sets confirmed the existence of such structures and located the transition structures for the insertion reaction. The calculated transition barrier is 10.0 kcal/mol for n = 9 and 7.1 kcal/mol for n = 8 at the MP2/6-31G** level, with zero-point energy corrections. Second, the experimentally observed size-dependent H(2) elimination reaction is related to the conformation of HAlOH(+)(H(2)O)(n-1), instead of Al(+)(H(2)O)(n). As n increases from 6 to 14, the structure of the HAlOH(+)(H(2)O)(n-1) cluster changes into a caged structure, with the Al-H bond buried inside, and protons produced in acidic dissociation could then travel through the H(2)O network to the vicinity of the Al-H bond and react with the hydride H to produce H(2). The structural transformation is completed at n = 13, coincident approximately with the onset of the H(2) elimination reaction. From constrained ab initio MD simulations, we estimated the free energy barrier for the H(2) elimination reaction to be 0.7 eV (16 kcal/mol) at n = 13, 1.5 eV (35 kcal/mol) at n = 12, and 4.5 eV (100 kcal/mol) at n = 8. The existence of transition structures for the H(2) elimination has also been verified by ab initio calculations at the MP2/6-31G** level. Finally, the switch-off of the H(2) elimination for n > 24 is explored and attributed to the diffusion of protons through enlarged hydrogen bonded H(2)O networks, which reduces the probability of finding a proton near the Al-H bond.     

Ab initio and DFT studies of the vibrational spectra of hydrogen-bonded PhOH...(H2O)4 complexes

The vibrational characteristics (vibrational frequencies and infrared intensities) for the hydrogen-bonded complex of phenol with four water molecules PhOH...(H2O)4 (structure 4A) have been predicted using ab initio and DFT (B3LYP) calculations with 6-31G(d,p) basis set. The changes in the vibrational characteristics from free monomers to a complex have been calculated. The ab initio and B3LYP calculations show that the observed four intense bands at 3299, 3341, 3386 and 3430 cm(-1) can be assigned to the hydrogen-bonded OH stretching vibrations in the complex PhOH...(H2O)4 (4A). The complexation leads to very large red shifts of these vibrations and very strong increase in their IR intensity. The predicted red shifts for these vibrations with B3LYP/6-31G(d,p) calculations are in very good agreement with the experimentally observed. It was established that the phenolic OH stretching vibration is the most sensitive to the hydrogen bonding. The predicted red-shift with the B3LYP/6-31G(d,p) calculations for the most stable ring structure 4A (-590 cm(-1)) is in better agreement with the experimentally observed than the red-shift, predicted with SCF/6-31G(d,p) calculations. The magnitude of the wavenumber shift is indicative of relatively strong OH...H hydrogen-bonded interaction. The complexation between phenol and four water molecules leads to strong increase of the IR intensity of the phenolic OH stretching vibration (up to 38 times).     

Experiments and quantum-chemical calculations on Rydberg states of H2CS in the region 5.6-9.5 eV

Absorption spectrum of H(2)CS in the region 5.6-9.5 eV was recorded with a continuously tunable light source of synchrotron radiation. After we subtracted absorption bands of CS(2), our spectrum clearly shows vibrational progressions associated with transitions (1)A(1)(pi,pi*)-X (1)A(1) and (1)B(2)(n,4s)-X (1)A(1) in the region 5.6-6.7 eV. A spectrum from which absorption of C(2)H(4) and CS(2) are subtracted shows several discrete bands in the region 6.9-9.5 eV. A Rydberg state (1)B(2)(n,4p(z)) lying below Rydberg state (1)A(1)(n,4p(y)) is confirmed, and the C-H symmetric stretching (nu(1)) and CH out-of-plane bending (nu(4)) modes for a transition (1)B(2)(n,4s)-X (1)A(1) are identified. New transitions to Rydberg states associated with excitation to 5s-11s, 5p(z)-7p(z), 5p(y)-7p(y), and 3d-6d are identified based on quantum defects and comparison with vertical excitation energies predicted with time-dependent density-functional theory (TD-DFT) and outer-valence Green's-function (OVGF) methods. For lower excited states predictions from these TD-DFT6-31+G calculations agree satisfactorily with experimental values, but for higher Rydberg states the OVGF method using aug-cc-pVTZ basis set augmented with extra diffuse functions yields more accurate predictions of excitation energies.     

Comparison of ab initio and DFT electronic structure methods for peptides containing an aromatic ring: effect of dispersion and BSSE

We establish that routine B3LYP and MP2 methods give qualitatively wrong conformations for flexible organic systems containing pi systems and that recently developed methods can overcome the known inadequacies of these methods. This is illustrated for a molecule (a conformer of the Tyr-Gly dipeptide) for which B3LYP/6-31+G(d) and MP2/6-31+G(d) geometry optimizations yield strikingly different structures [Mol. Phys. 2006, 104, 559-570]: MP2 predicts a folded "closed-book" conformer with the glycine residue located above the tyrosine ring, whereas B3LYP predicts a more open conformation. By employing different levels of theory, including the local electron correlation methods LMP2 (local MP2) and LCCSD(T0) (local coupled cluster with single, double, and noniterative local triple excitations) and large basis sets (aug-cc-pVnZ, n=D, T, Q), it is shown that the folded MP2 minimum is an artifact caused by large intramolecular BSSE (basis set superposition error) effects in the MP2/6-31+G(d) calculations. The B3LYP functional gives the correct minimum, but the potential energy apparently rises too steeply when the glycine and tyrosine residues approach each other, presumably due to missing dispersion effects in the B3LYP calculations. The PWB6K and M05-2X functionals, designed to give good results for weak interactions, remedy this to some extent. The reduced BSSE in the LMP2 calculations leads to faster convergence with increasing basis set quality, and accurate results can be obtained with smaller basis sets as compared to canonical MP2. We propose LMP2 as a suitable method to study interactions with pi-electron clouds.     

Application of a structure/oxidation-state correlation to complexes of bridging azo ligands

Based on data from more than 40 crystal structures of metal complexes with azo-based bridging ligands (2,2'-azobispyridine, 2,2'-azobis(5-chloropyrimidine), azodicarbonyl derivatives), a correlation between the N?N bond lengths (d(NN) ) and the oxidation state of the ligand (neutral, neutral/back-donating, radical-anionic, dianionic) was derived. This correlation was applied to the analysis of four ruthenium compounds of 2,2'-azobispyridine (abpy), that is, the new asymmetrical rac-[(acac)(2) Ru1(μ-abpy)Ru2(bpy)(2) ](ClO(4) )(2) ([1](ClO(4) )(2) ), [Ru(acac)(2) (abpy)] (2), [Ru(bpy)(2) (abpy)](ClO(4) )(2) ([3](ClO(4) )(2) ), and meso-[(bpy)(2) Ru(μ-abpy)Ru(bpy)(2) ](ClO(4) )(3) ([4](ClO(4) )(3) ; acac(-) =2,4-pentanedionato, bpy=2,2'-bipyridine). In agreement with DFT calculations, both mononuclear species 2 and 3(2+) can be described as ruthenium(II) complexes of unreduced abpy(0) , with 1.295(5)相似文献