True stabilization energies for the optimal planar hydrogen-bonded and stacked structures of guanine...cytosine, adenine...thymine, and their 9- and 1-methyl derivatives: complete basis set calculations at the MP2 and CCSD(T) levels and comparison with experiment

Planar H-bonded and stacked structures of guanine...cytosine (G.C), adenine...thymine (A...T), 9-methylguanine...1-methylcytosine (mG...mC), and 9-methyladenine...1-methylthymine (mA...mT) were optimized at the RI-MP2 level using the TZVPP ([5s3p2d1f/3s2p1d]) basis set. Planar H-bonded structures of G...C, mG...mC, and A...T correspond to the Watson-Crick (WC) arrangement, in contrast to mA...mT for which the Hoogsteen (H) structure is found. Stabilization energies for all structures were determined as the sum of the complete basis set limit of MP2 energies and a (DeltaE(CCSD(T)) - DeltaE(MP2)) correction term evaluated with the cc-pVDZ(0.25,0.15) basis set. The complete basis set limit of MP2 energies was determined by two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T and X = T and Q. This procedure is required since the convergency of the MP2 interaction energy for the present complexes is rather slow, and it is thus important to include the extrapolation to the complete basis set limit. For the MP2/aug-cc-pVQZ level of theory, stabilization energies for all complexes studied are already very close to the complete basis set limit. The much cheaper D-->T extrapolation provided a complete basis set limit close (by less than 0.7 kcal/mol) to the more accurate T-->Q term, and the D-->T extrapolation can be recommended for evaluation of complete basis set limits of more extended complexes (e.g. larger motifs of DNA). The convergency of the (DeltaE(CCSD(T)) - DeltaE(MP2)) term is known to be faster than that of the MP2 or CCSD(T) correlation energy itself, and the cc-pVDZ(0.25,0.15) basis set provides reasonable values for planar H-bonded as well as stacked structures. Inclusion of the CCSD(T) correction is essential for obtaining reliable relative values for planar H-bonding and stacking interactions; neglecting the CCSD(T) correction results in very considerable errors between 2.5 and 3.4 kcal/mol. Final stabilization energies (kcal/mol) for the base pairs studied are very substantial (A...T WC, 15.4; mA...mT H, 16.3; A...T stacked, 11.6; mA...mT stacked, 13.1; G...C WC, 28.8; mG...mC WC, 28.5; G...C stacked, 16.9; mG...mC stacked, 18.0), much larger than published previously. On the basis of comparison with experimental data, we conclude that our values represent the lower boundary of the true stabilization energies. On the basis of error analysis, we expect the present H-bonding energies to be fairly close to the true values, while stacked energies are still expected to be about 10% too low. The stacking energy for the mG...mC pair is considerably lower than the respective H-bonding energy, but it is larger than the mA...mT H-bonding energy. This conclusion could significantly change the present view on the importance of specific H-bonding interactions and nonspecific stacking interactions in nature, for instance, in DNA. Present stabilization energies for H-bonding and stacking energies represent the most accurate and reliable values and can be considered as new reference data.     

Improper hydrogen bonded cyclohexane C-Hax···Yax contacts: theoretical predictions and experimental evidence from 1H NMR spectroscopy of suitable axial cyclohexane models

C-H(ax)···Y(ax) contacts are a textbook prototype of steric hindrance in organic chemistry. The nature of these contacts is investigated in this work. MP2/6-31+G(d,p) calculations predicted the presence of improper hydrogen bonded C-H(ax)···Y(ax) contacts of different strength in substituted cyclohexane rings. To support the theoretical predictions with experimental evidence, several synthetic 2-substituted adamantane analogues (1-24) with suitable improper H-bonded C-H(ax)···Y(ax) contacts of different strength were used as models of a substituted cyclohexane ring. The (1)H NMR signal separation, Δδ(γ-CH(2)), within the cyclohexane ring γ-CH(2)s is raised when the MP2/6-31+G(d,p) calculated parameters, reflecting the strength of the H-bonded C-H(ax)···Y(ax) contact, are increased. In molecules with enhanced improper H-bonded contacts C-H(ax)···Y(ax), like those having sterically crowded contacts (Y(ax) = t-Bu) or contacts including considerable electrostatic attractions (Y(ax) = O-C or O═C) the calculated DFT steric energies of the γ-axial hydrogens are considerably reduced reflecting their electron cloud compression. The results suggest that the proton H(ax) electron cloud compression, caused by the C-H(ax)···Y(ax) contacts, and the resulting increase in Δδ(γ-CH(2)) value can be effected not just from van der Waals spheres compression, but more generally from electrostatic attraction forces and van der Waals repulsion, both of which are improper H-bonding components.     

A theoretical study on three conformational structures of 2,6‐distyrylpyridine

Ab initio methods at the levels HF/cc‐pVDZ, HF/6‐31G(d,p), MP2/cc‐pVDZ, and MP2/6‐31G(d,p), as well as methods based on density functional theory (DFT) employing the hybrid functional B3LYP with the basis sets cc‐pVDZ and 6‐31G(d,p), have been applied to study the conformers of 2,6‐distyrylpyridine. Bond distances, bond angles, and dihedral angles have been calculated at the B3LYP level. The calculated values were in good agreement with those measured by X‐ray diffraction analysis of 2,6‐distyrylpyridine. The values calculated using the Hartree‐Fock method and second‐order perturbation theory (MP2) were inconsistent. The optimized lowest‐energy geometries were calculated from the reported X‐ray structural data by the B3LYP/cc‐pVDZ method. Three conformations, A, B, and C, were proposed for 2,6‐distyrylpyridine. Calculations at the three levels of theory indicated that conformation A was the most stable structure, with conformations C and B being higher in energy by 1.10 and 2.57 kcal/mol, respectively, using the same method and basis function. The same trend in the relative energies of the three possible conformations was observed at the two levels of theory and with the different basis sets employed. The reported X‐ray data were utilized to optimize total molecular energy of conformation A at the different calculation levels. The bond lengths, bond angles, and dihedral angles were then obtained from the optimized geometries by ab initio methods and by applying DFT using the two basis functions cc‐pVDZ and 6‐31G(d,p). The values were analyzed and compared. The calculated total energies, the relative energies of the molecular orbitals, the gap between them, and the dipole moment for each conformational structure proposed for 2,6‐distyrylpyridine are also reported. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

On differences between hydrogen bonding and improper blue-shifting hydrogen bonding.

Twenty two hydrogen-bonded and improper blue-shifting hydrogen-bonded complexes were studied by means of the HF, MP2 and B3LYP methods using the 6-31G(d,p) and 6--311 ++G(d,p) basis sets. In contrast to the standard H bonding, the origin of the improper blue-shifting H bonding is still not fully understood. Contrary to a frequently presented idea, the electric field of the proton acceptor cannot solely explain the different behavior of the H-bonded and improper blue-shifting H-bonded complexes. Compression of the hydrogen bond due to different attractive forces-dispersion or electrostatics--makes an important contribution as well. The symmetry-adapted perturbation theory (SAPT) has been utilized to decompose the total interaction energy into physically meaningful contributions. In the red-shifting complexes, the induction energy is mostly larger than the dispersion energy while, in the case of blue-shifting complexes, the situation is opposite. Dispersion as an attractive force increases the blue shift in the blue-shifting complexes as it compresses the H bond and, therefore, it increases the Pauli repulsion. On the other hand, dispersion in the red-shifting complexes increases their red shift.     

M(CN)(2) Species (M = Be, Mg, Ca, Sr, Ba): Cyanides, Nitriles, or Neither?

The "cyanide" salts of the group 2 (alkaline earth) metals exhibit remarkable structural variations: CN(-) binds to the metals via the carbon, via the nitrogen, and via bridged arrangements. The most stable geometries of the beryllium and the magnesium salts are linear (CNBeNC and NCMgCN, respectively), but CaC(2)N(2), SrC(2)N(2), and BaC(2)N(2) prefer twisted, bridged structures. However, several stationary points of the bridged complexes are close in energy, and considerable fluxionality is to be expected. These theoretical predictions (MP4SDTQ/6-311+G(2d)//MP2(fu)/6-31+G, Ca, Sr, Ba: 5s5p3d1f//5s5p3d basis sets and 10 valence electron pseudopotentials) invite experimental verification.     

Rotational spectrum of 1,1,1-trifluoro-2-butanone using chirped-pulse Fourier transform microwave spectroscopy

The pure rotational spectra of 1,1,1-trifluoro-2-butanone and its four (13)C isotopologues have been studied using the new chirped-pulsed Fourier transform microwave spectrometer at the University of Manitoba in combination with a conventional Balle-Flygare-type instrument. Quantum chemical calculations, at the MP2/6-311++G(d,p) level, were carried out to obtain information about the structure, relative stability, and difference in populations of the three lowest energy conformers corresponding to dihedral angles of 0°, 82.8°, and 119.2° along the carbon backbone. The observed spectra are that of conformer I (dihedral angle 0°), and, based on analysis of the observed splitting, the V(3) barrier to internal rotation of the methyl group has been determined to be 9.380(5) kJ mol(-1). The spectroscopic constants of the five isotopologues were used to precisely derive the r(s) and partial r(0) geometries of this conformer based on an assumed planar carbon backbone (as supported by the spectra and ab initio calculations).     

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations

A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages. In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged elastic band methods, which are powerful techniques for studying reaction pathways in a highly parallel (i.e., parallel/parallel) fashion, with each pathway point being distributed to a different node of a large cluster. To test our implementation, a series of systems were studied and comparisons were made to both full QM calculations and previous QM/MM studies and experiments. For instance, the differences between HF, DFT, MP2, and CCSD QM/MM calculations of H2O...H2O, H2O...Na+, and H2O...Cl- complexes have been explored. Furthermore, the recently implemented polarizable Drude water model was used to make comparisons to the popular TIP3P and TIP4P water models for doing QM/MM calculations. We have also computed the energetic profile of the chorismate mutase catalyzed Claisen rearrangement at various QM/MM levels of theory and have compared the results with previous studies. Our best estimate for the activation energy is 8.20 kcal/mol and for the reaction energy is -23.1 kcal/mol, both calculated at the MP2/6-31+G(d)//MP2/6-31+G(d)/C22 level of theory.     

Improper hydrogen-bonded cyclohexane C-Hax?Yax contacts: experimental evidence from H NMR spectroscopy of suitable axial cyclohexane models

B3LYP/6-31+G(d,p) calculations predicted the presence of improper hydrogen-bonded C-H_ax?Y_ax contacts of different strength in cyclohexane derivatives;¹ it was predicted that the addition of an appropriate bridging fragment X_ax between an axial substituent Y₁ and a cyclohexane carbon would strengthen the improper hydrogen-bonded contact C-H_ax?Y₁ when the X_ax-Y₁ bond vector bisects the cyclohexane ring. To support the theoretical predictions with experimental evidence for this effect, several 2-substituted adamantane analogues with suitable improper H-bonded C-H_ax?O contacts of different strength were synthesized, as models of the corresponding cyclohexane derivatives, and their ¹H NMR spectra were recorded at 298 K. The ¹H NMR signal separation within the cyclohexane ring γ-CH₂s is increased when the B3LYP/6-31+G(d,p)-calculated strength of the H-bonded C-H_ax?O=C_ax contact interaction is increased.     

CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates

Presented is an extension of the CHARMM additive all-atom carbohydrate force field to enable the modeling of phosphate and sulfate linked to carbohydrates. The parameters are developed in a hierarchical fashion using model compounds containing the key atoms in the full carbohydrates. Target data for parameter optimization included full two-dimensional energy surfaces defined by the glycosidic dihedral angle pairs in the phosphate/sulfate model compound analogs of hexopyranose monosaccharide phosphates and sulfates, as determined by quantum mechanical (QM) MP2/cc-pVTZ single point energies on MP2/6-31+G(d) optimized structures. In order to achieve balanced, transferable dihedral parameters for the dihedral angles, surfaces for all possible anomeric and conformational states were included during the parametrization process. In addition, to model physiologically relevant systems both the mono- and di-anionic charged states were studied for the phosphates. This resulted in over 7000 MP2/cc-pVTZ//MP2/6-31G+(d) model compound conformational energies which, supplemented with QM geometries, were the main target data for the parametrization. Parameters were validated against crystals of relevant monosaccharide derivatives obtained from the Cambridge Structural Database (CSD) and larger systems, namely inositol-(tri/tetra/penta) phosphates non-covalently bound to the pleckstrin homology (PH) domain and oligomeric chondroitin sulfate in solution and in complex with cathepsin K protein.     

Scope and limitations of the SCS-MP2 method for stacking and hydrogen bonding interactions

Fluorobenzenes are pi-acceptor synthons that form pi-stacked structures in molecular crystals as well as in artificial DNAs. We investigate the competition between hydrogen bonding and pi-stacking in dimers consisting of the nucleobase mimic 2-pyridone (2PY) and all fluorobenzenes from 1-fluorobenzene to hexafluorobenzene (n-FB, with n = 1-6). We contrast the results of high level ab initio calculations with those obtained using ultraviolet (UV) and infrared (IR) laser spectroscopy of isolated and supersonically cooled dimers. The 2PY.n-FB complexes with n = 1-5 prefer double hydrogen bonding over pi-stacking, as diagnosed from the UV absorption and IR laser depletion spectra, which both show features characteristic of doubly H-bonded complexes. The 2-pyridone.hexafluorobenzene dimer is the only pi-stacked dimer, exhibiting a homogeneously broadened UV spectrum and no IR bands characteristic for H-bonded species. MP2 (second-order M?ller-Plesset perturbation theory) calculations overestimate the pi-stacked dimer binding energies by about 10 kJ/mol and disagree with the experimental observations. In contrast, the MP2 treatment of the H-bonded dimers appears to be quite accurate. Grimme's spin-component-scaled MP2 approach (SCS-MP2) is an improvement over MP2 for the pi-stacked dimers, reducing the binding energy by approximately 10 kJ/mol. When applied to explicitly correlated MP2 theory (SCS-MP2-R12 approach), agreement with the corresponding coupled-cluster binding energies [at the CCSD(T) level] is very good for the pi-stacked dimers, within +/- 1 kJ/mol for the 2PY complexes with 1-fluorobenzene, 1,2-difluorobenzene, 1,2,4,5-tetrafluorobenzene, pentafluorobenzene and hexafluorobenzene. Unfortunately, the SCS-MP2 approach also reduces the binding energy of the H-bonded species, leading to disagreement with both coupled-cluster theory and experiment. The SCS-MP2-R12 binding energies follow the SCS-MP2 binding energies closely, being about 0.5 and 0.7 kJ/mol larger for the H-bonded and pi-stacked forms, respectively, in an augmented correlation-consistent polarized valence quadruple-zeta basis. It seems that the SCS-MP2 and SCS-MP2-R12 methods cannot provide sufficient accuracy to replace the CCSD(T) method for intermolecular interactions where H-bonding and pi-stacking are competitive.     

Multiply Borylated Arenes: X‐ray Crystal Structure Analyses and Quantum Chemical Calculations

Optimised synthesis procedures and results of X‐ray single crystal structure analyses for 4‐(dibromoboryl)toluene, 1, 3‐bis(dibromoboryl)benzene, 1, 4‐bis(dibromoboryl)benzene, and 1, 3, 5‐tris(dibromoboryl)benzene are reported. These compounds have also been studied by Hartree‐Fock (HF), density functional theory (DFT), and Mßller‐Plesset second‐order perturbation (MP2) methods in combination with the polarized double‐ζ valence (SVP) and polarized triple‐ζ valence (TZVP) basis sets of Ahlrichs and coworkers. A comparison of the quantum chemical results for optimised geometries and computed NMR chemical shifts with experiment is presented to test the quality of the various methods for this class of compounds. All DFT methods tested yield optimised geometries within the experimental error bars of 3σ for bond lengths, whereas larger deviations among the methods are observed for computed NMR chemical shifts. This calibration recommends the B3LYP/SVP combination as a reliable and computationally efficient level of theory to assess the structures and absolute and relative ¹H‐, ¹³C‐ and ¹¹B NMR shift values of borylated aromatic compounds in future investigations.     

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.     

Single-conformation ultraviolet and infrared spectroscopy of model synthetic foldamers: beta-peptides Ac-beta3-hPhe-NHMe and Ac-beta3-hTyr-NHMe

The conformational preferences and infrared and ultraviolet spectral signatures of two model beta-peptides, Ac-beta3-hPhe-NHMe (1) and Ac-beta3-hTyr-NHMe (2), have been explored under jet-cooled, isolated molecule conditions. The mass-resolved, resonant two-photon ionization spectra of the two molecules were recorded in the region of the S0-S1 origin of the phenyl or phenol ring substituents, respectively. UV-UV hole-burning spectroscopy was used to determine that two conformations of 1 are present, with the transitions due to conformer A, with S0-S1 origin at 34431 cm(-1), being almost 20 times larger than those due to conformer B, with S0-S1 origin at 34404 cm(-1). Only one conformation of 2 was observed. Resonant ion-dip infrared spectroscopy provided single-conformation infrared spectra in the 3300-3700 cm(-1) region. The spectra of conformer A of both molecules have H-bonded and free amide NH stretch infrared transitions at 3400 and 3488 cm(-1), respectively, while conformer B of 1 possesses bands at 3417 and 3454 cm(-1). For comparison with experiment, full optimizations of all low-lying minima of 1 were carried out at the DFT B3LYP/6-31+G* and RIMP2/aug-cc-pVDZ levels of theory, and single point MP2/6-31+G* calculations at the DFT geometries. On the basis of the comparison with previous studies in solution and the calculated results, conformer A of 1 and 2 were assigned to a C6 conformer, while conformer B of 1 was assigned to a unique C8 structure with a weak intramolecular H-bond. The reasons for the preference for C6 over C8 structures and the presence of only two conformations in the jet-cooled spectrum are discussed in light of the predictions from calculations.     

At nonzero temperatures, stacked structures of methylated nucleic acid base pairs and microhydrated nonmethylated nucleic acid base pairs are favored over planar hydrogen-bonded structures: a molecular dynamics simulations study

The dynamic structure of all ten possible nucleic acid (NA) base pairs and methylated NA base pairs hydrated by a small number of water molecules (from 1 to 16) was determined by using molecular dynamics simulations in the NVE microcanonical and NVT canonical ensembles with the Cornell force field (W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. E. Caldwell, P. Kollman, J. Am. Chem. Soc. 1995, 117, 5179). The presence of one water molecule does not affect the structure of any hydrogen-bonded (H-bonded) nonmethylated base pair. An equal population of H-bonded and stacked structures of adenine...adenine, adenine...guanine and adenine... thymine pairs is reached if as few as two water molecules are present, while obtaining equal populations of these structures in the case of adenine...cytosine, cytosine...thymine, guanine... guanine and guanine...thymine required the presence of four water molecules, and in the case of guanine...cytosine, six. A comparable population of planar, H-bonded and stacked structures for cytosine...cytosine and thymine... thymine base pairs was only obtained if at least eight water molecules hydrated a pair. Methylation of bases changed the situation dramatically and stacked structures were favoured over H-bonded ones even in the absence of water molecules in most cases. Only in the case of methyl cytosine...methyl cytosine, methyl guanine...methyl guanine and methyl guanine...methyl cytosine pairs were two, two or six water molecules, respectively, needed in order to obtain a comparable population of planar, H-bonded and stacked structures. We believe that these results give clear evidence that the preferred stacked structure of NA base pairs in the microhydrated environment, and also apparently in a regular solvent, is due to the hydrophilic interaction of a small number of water molecules. In the case of methylated bases, it is also due to the fact that the hydrogen atoms most suitable for the formation of H-bonds have been replaced by a methyl group. A preferred stacked structure is, thus, not due to a hydrophobic interaction between a large bulk of water molecules and the base pair, as believed.     

分子几何构型优化方法的系统性比较

对《ＣＲＣ物理化学手册》第７７版中收集的第三周期以前的所有已知实验构型的无机分子的构型,以ＭＰ２、Ｂ３ＬＹＰ、Ｂ３ＰＷ９１级别上进行了构型优化的系统性比较,优化采用基组为６－３１Ｇ（ｄ,ｐ）,６－３１１Ｇ（ｄ,ｐ）,６－３１１Ｇ（２ｄ,ｐ）。对大多数分子另比较了ＱＣＩＳＤ（Ｔ）方法,对多原子分子比较了ＢＰＷ９１方法,对含氢双原子分子也使用ＱＣＩＳＤ方法。结果表明,键长的平均绝对偏差（单位：ｐｐｍ）     

The structures of the azido-, isocyanato- and isothiocyanato- derivatives of methane and silane and their derivatives. A comparison of ab initio with experimental results

The equilibrium structures of various conformers of the azides, isocyanates and isothiocyanates with general type Me_3−nH_nW–N=X=Y, together with a small number of their halogenated derivatives, have been determined by Möller–Plessett (MP2) calculations under standard triple zeta valence + polarisation basis set conditions. The structures are compared with each other, with previous and other theoretical studies including CCSD(T) results, and with experimental spectral and diffraction results. The MP2 and CCSD(T) results correlate strongly for a series of these molecules; thus the CCSD(T) bond lengths are larger by about 1.9%. The angles are little different, partly as a result of balancing effects; where some CNN and CNC angles are smaller in CCSD(T) by 2–3°, but some CCSD(T) dihedral angles HCNN and HCNC are larger. The MP2 results for the wider group correlate closely with microwave and infrared spectra, and with electron diffraction data. In contrast, the B3LYP method, with the same bases, whilst apparently giving reasonable structures, gives very poor rotation constants, as a result of poor CNC angle determination. The present results suggest that the spectra of ethyl isocyanate, silyl azide, trimethylsilyl azide, and silyl isocyanate require reinvestigation. This is part of a wider study where the central atom W is the series of Group 14 tetrahedral atoms up to Pb; in this study, the central atom W is C and Si, with XY either N=N, C=O or C=S.     

Molecular and electronic structure of δ-valerothiolactone

The crystal structure of the six-member heterocyclic δ-valerothiolactone (1-thiocycloalkan-2-one) compound has been determined by X-ray diffraction at low temperature, revealing that its skeleton adopts a half-chair conformation. The conformation around the thioester group is almost planar with an anti orientation of the C=O double bond with respect the S-C single bond [C(2)-S(1)-C(6)-O(1) = 176.26(8)°]. The skeletal parameters, especially valence angles [∠C5-C6-S = 121.19(6)°, ∠O=C6-C5 = 122.25(8)°, ∠C6-S-C2 = 106.80(4)°], differ from those typically found in acyclic thioester compounds, symptomatic of the presence of strain effects. The conventional ring strain energy was determined to be 7.5 kcal/mol at the MP2/6-311++G(d,p) level of calculation within the hyperhomodesmotic model approximation. Moreover, the valence electronic structure was investigated by HeI photoelectron spectroscopy assisted by quantum chemical calculations at the OVGF/6-311++G(d,p) level of theory. The first three bands at 9.35, 9.50, and 11.53 eV denote ionizations related with the n(S), n(O), and π(C=O) orbitals, respectively, demonstrating the importance of the -SC(O)- group in the outermost electronic properties.     

An ab initio benchmark study of hydrogen bonded formamide dimers

The five singly and doubly hydrogen bonded dimers of formamide are calculated at the correlated level by using resolution of identity M?ller-Plesset second-order perturbation theory (RIMP2) and the coupled cluster with singles, doubles, and perturbative triples [CCSD(T)] method. All structures are optimized with the Dunning aug-cc-pVTZ and aug-cc-pVQZ basis sets. The binding energies are extrapolated to the complete basis set (CBS) limit by using the aug-cc-pVXZ (X = D, T, Q) basis set series. The effect of extending the basis set to aug-cc-pV5Z on the geometries and binding energies is studied for the centrosymmetric doubly N-H...O bonded dimer FA1 and the doubly C-H...O bonded dimer FA5. The MP2 CBS limits range from -5.19 kcal/mol for FA5 to -14.80 kcal/mol for the FA1 dimer. The DeltaCCSD(T) corrections to the MP2 CBS limit binding energies calculated with the 6-31+G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are mutually consistent to within < or =0.03 kcal/mol. The DeltaCCSD(T) correction increases the binding energy of the C-H...O bonded FA5 dimer by 0.4 kcal/mol or approximately 9% over the distance range +/-0.5 Angstrom relative to the potential minimum. This implies that the ubiquitous long-range C-H...O interactions in proteins are stronger than hitherto calculated.     

Ab initio study of some peroxides. HOOH, CH3OOH and, CH3OOCH3

The geometries of HOOH, CH₃OOH, and CH₃OOCH₃, were optimized with different basis sets (3-21G, 6-31G^*(*) and D95^**) at different levels of theory (HF, MP2, MP4, and CI). HF/3-21G optimizations result in planar trans conformations for all three peroxides. HF/6-31G^** calculations predict skew conformations for HOOH and CH₃OOH, but a planar trans struture for CH₃OOCH₃. For the larger basis set the calculated bond lengths, especially the O-O bonds, are too short. Optimizations for HOOH including electron correlation at the MP2, MP3, MP4, CI, and CCD level improve the agreement for bond lengths and the OOH angle, but result in dihedral angles Which are too large by 3– 8°. In the case of CH₃OOCH₃, similar calculations at the MP2 and CI level predict planar trans structures instead of the experimentally observed skew conformation. On the other hand, MP4 single point calculations at MP2 optimized parameters result in a correct skew structure. For all three peroxides a computationally “economic” method, i.e., single point calculations at MP2 or MP4 level with HF/3-21G optimized parameters, result in close agreement between calculated and experimental structures.     

A theoretical study of hydrogen- and lithium-bonded complexes of F-H∕Li and Cl-H∕Li with NF3, NH3, and NH2(CH3)

Hydrogen- and lithium-bonded complexes of A-H∕Li (A = F, Cl) with the amine analogues NF(3), NH(3), and NH(2)(CH(3)) were studied at the MP2∕6-311++G(d,p) level of theory. Bond extensions and redshifts were obtained for the H-bonded complexes, while bond extensions and blueshifts were obtained for the Li-bonded species. The variation of these and other properties with the basicity of the amines was investigated and rationalized by comparing the ab initio results with predictions from a model derived from perturbation theory.