Combining explicitly correlated R12 and Gaussian geminal electronic structure theories

Explicitly correlated R12 methods using a single short-range correlation factor (also known as F12 methods) have dramatically smaller basis set errors compared to the standard wave function counterparts, even when used with small basis sets. Correlations on several length scales, however, may not be described efficiently with one correlation factor. Here the authors explore a more general MP2-R12 method in which each electron pair uses a set of (contracted) Gaussian-type geminals (GTGs) with fixed exponents, whose coefficients are optimized linearly. The following features distinguish the current method from related explicitly correlated approaches published in the literature: (1) only two-electron integrals are needed, (2) the only approximations are the resolution of the identity and the generalized Brillouin condition, (3) only linear parameters are optimized, and (4) an arbitrary number of (non-)contracted GTGs can appear. The present method using only three GTGs and a double-zeta quality basis computed valence correlation energies for a set of 20 small molecules only 2.2% removed from the basis set limit. The average basis set error reduces to 1.2% using a near-complete set of seven GTGs with the double-zeta basis set. The conventional MP2 energies computed with much larger quadruple, quintuple, and sextuple basis sets all had larger average errors: 4.6%, 2.4%, and 1.5%, respectively. The new method compares well to the published MP2-R12 method using a single Slater-type geminal (STG) correlation factor. For example, the average basis set error in the absolute MP2-R12 energy obtained with the exp(-r12) correlation factor is 1.7%. Correlation contribution to atomization energies evaluated with the present method and with the STG-based method only required a double-zeta basis set to exceed the precision of the conventional sextuple-zeta result. The new method is shown to always be numerically stable if linear dependencies are removed from the two-particle basis and the zeroth-order Hamiltonian matrix is made positive definite.     

Analyzing Pt chemical shifts calculated from relativistic density functional theory using localized orbitals: the role of Pt 5d lone pairs

Pt chemical shifts were calculated from two-component relativistic density functional theory (DFT). The shielding tensors were analyzed by using a recently developed method to decompose the spin-orbit DFT results into contributions from spin-free localized orbitals (here: natural localized molecular orbitals (NLMOs) and natural bond orbitals (NBOs)). Seven chemical shifts in six Pt complexes with Pt oxidation states II, III, and IV; and halide, amino, and amidate ligands were analyzed, with particular focus on the role of nonbonding Pt 5d orbitals. A simple d-orbital 'rotation' model has been used to rationalize some of the observed trends such as the main difference between Pt(II) and Pt(IV) chemical shifts. The localized orbital analysis data showed that most of this difference as well as trends among different Pt complexes with similar coordination can be rationalized by comparing properties of the nonbonding Pt 5d orbitals. We have also analyzed the spin-orbit effects on the chemical shifts of [PtCl4](2-) compared to [PtBr4](2-).     

Relativistic calculations of ground and excited states of LiYb molecule for ultracold photoassociation spectroscopy studies

We report a series of quantum-chemical calculations for the ground and some of the low-lying excited states of an isolated LiYb molecule by the spin-orbit multistate complete active space second-order perturbation theory (SO-MS-CASPT2). Potential energy curves, spectroscopic constants, and transition dipole moments (TDMs) at both spin-free and spin-orbit levels are obtained. Large spin-orbit effects especially in the TDMs of the molecular states dissociating to Yb((3)P(0,1,2)) excited states are found. To ensure the reliability of our calculations, we test five types of incremental basis sets and study their effect on the equilibrium distance and dissociation energy of the ground state. We also compare CASPT2 and CCSD(T) results for the ground state spectroscopic constants at the spin-free relativistic level. The discrepancies between the CASPT2 and CCSD(T) results are only 0.01 ? in equilibrium bond distance (R(e)) and 200 cm(-1) in dissociation energy (D(e)). Our CASPT2 calculation in the supermolecular state (R=100 a.u.) with the largest basis set reproduces experimental atomic excitation energies within 3% error. Transition dipole moments of the super molecular state (R=100 a.u.) dissociating to Li((2)P) excited states are quite close to experimental atomic TDMs as compared to the Yb((3)P) and Yb((1)P) excited states. The information obtained from this work would be useful for ultracold photoassociation experiments on LiYb.     

Perturbative correction for the basis set incompleteness error of complete-active-space self-consistent field

To reduce the basis set incompleteness of the complete-active-space self-consistent field (CASSCF) wave function and energy we develop a second-order perturbation correction due to single excitations to complete set of unoccupied states. Other than the one- and two-electron integrals, only one- and two-particle reduced density matrices are required to compute the correction, denoted as [2](S). Benchmark calculations on prototypical ground-state bond-breaking problems show that only the aug-cc-pVXZ basis is needed with the [2](S) correction to match the accuracy of CASSCF energies of the aug-cc-pV(X+1)Z quality.     

Comparison of one-particle basis set extrapolation to explicitly correlated methods for the calculation of accurate quartic force fields, vibrational frequencies, and spectroscopic constants: application to H2O, N2H+, NO2+, and C2H2

One-particle basis set extrapolation is compared with one of the new R12 methods for computing highly accurate quartic force fields (QFFs) and spectroscopic data, including molecular structures, rotational constants, and vibrational frequencies for the H(2)O, N(2)H(+), NO(2)(+), and C(2)H(2) molecules. In general, agreement between the spectroscopic data computed from the best R12 and basis set extrapolation methods is very good with the exception of a few parameters for N(2)H(+) where it is concluded that basis set extrapolation is still preferred. The differences for H(2)O and NO(2)(+) are small and it is concluded that the QFFs from both approaches are more or less equivalent in accuracy. For C(2)H(2), however, a known one-particle basis set deficiency for C-C multiple bonds significantly degrades the quality of results obtained from basis set extrapolation and in this case the R12 approach is clearly preferred over one-particle basis set extrapolation. The R12 approach used in the present study was modified in order to obtain high precision electronic energies, which are needed when computing a QFF. We also investigated including core-correlation explicitly in the R12 calculations, but conclude that current approaches are lacking. Hence core-correlation is computed as a correction using conventional methods. Considering the results for all four molecules, it is concluded that R12 methods will soon replace basis set extrapolation approaches for high accuracy electronic structure applications such as computing QFFs and spectroscopic data for comparison to high-resolution laboratory or astronomical observations, provided one uses a robust R12 method as we have done here. The specific R12 method used in the present study, CCSD(T)(R12), incorporated a reformulation of one intermediate matrix in order to attain machine precision in the electronic energies. Final QFFs for N(2)H(+) and NO(2)(+) were computed, including basis set extrapolation, core-correlation, scalar relativity, and higher-order correlation and then used to compute highly accurate spectroscopic data for all isotopologues. Agreement with high-resolution experiment for (14)N(2)H(+) and (14)N(2)D(+) was excellent, but for (14)N(16)O(2)(+) agreement for the two stretching fundamentals is outside the expected residual uncertainty in the theoretical values, and it is concluded that there is an error in the experimental quantities. It is hoped that the highly accurate spectroscopic data presented for the minor isotopologues of N(2)H(+) and NO(2)(+) will be useful in the interpretation of future laboratory or astronomical observations.     

Analytic functions for the three-body potential of the helium trimer

The three-body potential for the ground state of the helium trimer is determined by an extended geminal model. The basis set for the calculation is an uncontracted (19s,7p,6d,5f,4g,2h) set of Gaussian-type functions. Three different types of configurations were considered: (i) equilateral triangles, (ii) linear configurations with R12=R23, and (iii) a set of pseudorandom configurations. The interatomic distances were selected within the interval [3.0,9.0] bohrs. The computed points have been fitted to global potential functions. The fit is characterized by a maximum absolute error equal to 0.69 microEh and a mean error equal to -0.018 microEh.     

Simple coupled-cluster singles and doubles method with perturbative inclusion of triples and explicitly correlated geminals: The CCSD(T)R12 model

To approach the complete basis set limit of the "gold-standard" coupled-cluster singles and doubles plus perturbative triples [CCSD(T)] method, we extend the recently proposed perturbative explicitly correlated coupled-cluster singles and doubles method, CCSD(2)(R12) [E. F. Valeev, Phys. Chem. Chem. Phys. 8, 106 (2008)], to account for the effect of connected three-electron correlations. The natural choice of the zeroth-order Hamiltonian produces a perturbation expansion with rigorously separable second-order energy corrections due to the explicitly correlated geminals and conventional triple and higher excitations. The resulting CCSD(T)(R12) energy is defined as a sum of the standard CCSD(T) energy and an amplitude-dependent geminal correction. The method is technically very simple: Its implementation requires no modification of the standard CCSD(T) program and the formal cost of the geminal correction is small. We investigate the performance of the open-shell version of the CCSD(T)(R12) method as a possible replacement of the standard complete-basis-set CCSD(T) energies in the high accuracy extrapolated ab initio thermochemistry model of Stanton et al. [J. Chem. Phys. 121, 11599 (2004)]. Correlation contributions to the heat of formation computed with the new method in an aug-cc-pCVXZ basis set have mean absolute basis set errors of 2.8 and 1.0 kJmol when X is T and Q, respectively. The corresponding errors of the standard CCSD(T) method are 9.1, 4.0, and 2.1 kJmol when X=T, Q, and 5. Simple two-point basis set extrapolations of standard CCSD(T) energies perform better than the explicitly correlated method for absolute correlation energies and atomization energies, but no such advantage found when computing heats of formation. A simple Schwenke-type two-point extrapolation of the CCSD(T)(R12)aug-cc-pCVXZ energies with X=T,Q yields the most accurate heats of formation found in this work, in error on average by 0.5 kJmol and at most by 1.7 kJmol.     

Many-body interaction analysis: algorithm development and application to large molecular clusters

A completely automated algorithm for performing many-body interaction energy analysis of clusters (MBAC) [M. J. Elrodt and R. J. Saykally, Chem. Rev. 94, 1975 (1994); S. S. Xantheas, J. Chem. Phys. 104, 8821 (1996)] at restricted Hartree-Fock (RHF)/MA Plesset 2nd order perturbation theory (MP2)/density functional theory (DFT) level of theory is reported. Use of superior guess density matrices (DM's) for smaller fragments generated from DM of the parent system and elimination of energetically insignificant higher-body combinations, leads to a more efficient performance (speed-up up to 2) compared to the conventional procedure. MBAC approach has been tested out on several large-sized weakly bound molecular clusters such as (H(2)O)(n), n=8, 12, 16, 20 and hydrated clusters of amides and aldehydes. The MBAC results indicate that the amides interact more strongly with water than aldehydes in these clusters. It also reconfirms minimization of the basis set superposition error for large cluster on using superior quality basis set. In case of larger weakly bound clusters, the contributions higher than four body are found to be repulsive in nature and smaller in magnitude. The reason for this may be attributed to the increased random orientations of the interacting molecules separated from each other by large distances.     

Isotope effects in hydrogen-bonded complexes. Calculation of geometrical and vibrational characteristics of asymmetric isotopologues of [F(HF)2]-

The geometrical and vibrational characteristics of isolated H-bonded anionic complexes [FHFDF](-), [FHFTF](-), and [FDFTF](-) are calculated quantum-mechanically. The four-dimensional anharmonic vibrational problems are solved by the variational method using the potential energy and dipole moment surfaces calculated in the MP2/6-311++G(3df,3pd) approximation with the basis set superposition error taken into account. Changes in the bond lengths of molecular fragments LF (L = H, D, T) and in the distances between the F(-) anion and the centers of mass of LF are used as the vibrational coordinates. For each isotopologue, the vibrational energy levels, the transition frequencies and absolute intensities for the H-bond and L-F stretching vibrations are determined. To study the isotope effects on the geometrical parameters, the values of internuclear separations and the asymmetry parameter of the F(-)···L-F bridges, averaged over the ground state and several excited vibrational states, are calculated, as well as their standard deviations. The calculations revealed an extremely strong influence of anharmonic coupling between different vibrations on the absorption intensities and a significant mass-dependence of spectroscopic and structural parameters. The geometry and harmonic frequencies of KH(2)F(3), KD(2)F(3), and KHDF(3) are also calculated at a lower ab initio level. The results obtained for [FHFDF](-), [FHFTF](-), and [FDFTF](-) are compared with the available experimental data and the results of earlier calculations of the symmetric complexes [F(HF)(2)](-), [F(DF)(2)](-), and [F(TF)(2)](-) and complexes containing a positive K-meson.     

Coupled-cluster methods with perturbative inclusion of explicitly correlated terms: a preliminary investigation

We propose to account for the large basis-set error of a conventional coupled-cluster energy and wave function by a simple perturbative correction. The perturbation expansion is constructed by L?wdin partitioning of the similarity-transformed Hamiltonian in a space that includes explicitly correlated basis functions. To test this idea, we investigate the second-order explicitly correlated correction to the coupled-cluster singles and doubles (CCSD) energy, denoted here as the CCSD(2)(R12) method. The proposed perturbation expansion presents a systematic and easy-to-interpret picture of the "interference" between the basis-set and correlation hierarchies in the many-body electronic-structure theory. The leading-order term in the energy correction is the amplitude-independent R12 correction from the standard second-order M?ller-Plesset R12 method. The cluster amplitudes appear in the higher-order terms and their effect is to decrease the basis-set correction, in accordance with the usual experience. In addition to the use of the standard R12 technology which simplifies all matrix elements to at most two-electron integrals, we propose several optional approximations to select only the most important terms in the energy correction. For a limited test set, the valence CCSD energies computed with the approximate method, termed , are on average precise to (1.9, 1.4, 0.5 and 0.1%) when computed with Dunning's aug-cc-pVXZ basis sets [X = (D, T, Q, 5)] accompanied by a single Slater-type correlation factor. This precision is a roughly an order of magnitude improvement over the standard CCSD method, whose respective average basis-set errors are (28.2, 10.6, 4.4 and 2.1%). Performance of the method is almost identical to that of the more complex iterative counterpart, CCSD(R12). The proposed approach to explicitly correlated coupled-cluster methods is technically appealing since no modification of the coupled-cluster equations is necessary and the standard M?ller-Plesset R12 machinery can be reused.     

Novel pentagonal silicon rings and nanowheels stabilized by flat pentacoordinate carbon(s)

It is predicted by accurate density functional and coupled-cluster theory that planar [Si(5)C](2-) and [Si(5)C](1-) rings can be stabilized by flat pentacoordinate carbon-silicon bonds. The energy difference of the [Si(5)C](2-) dianion from the lowest energy three-dimensional isomer is about 12.2 kcal∕mol at the level of the density functional theory using the Becke 3-parameter (exchange), Lee, Yang and Parr functional, and the triple-ζ doubly polarized basis sets. Stable composite [Si(5)C](2) structures are formed either as nanowheels with axial C-C bonds of 1.51 A? or as isoenergetic pentagonal graphiticlike layers with double C-C distance (3.02 A?) and almost double aromaticity index, based on nucleus independent chemical shifts. Both of these structures are at least 12 kcal∕mol lower in energy than the lowest energy Si(10)C(2) structure reported in the literature, but about 5 kcal∕mol higher than the lowest energy structure found here.     

Hexanuclear cobalt carbonyl carbide clusters: the interplay between octahedral and trigonal prismatic structures

The six-vertex cobalt carbonyl clusters [Co6C(CO)n](2-) (n = 12, 13, 14, 15, 16) with an interstitial carbon atom have been studied by density functional theory (DFT). These DFT studies indicate that the experimentally known structure of [Co6C(CO)15](2-) consisting of a Co6 trigonal prism with each of its edges bridged by carbonyl groups is a particularly stable structure lying more than 20 kcal/mol below any other [Co6C(CO)15](2-) structure. Addition of a CO group to this [Co6C(CO)15](2-) structure gives the lowest energy [Co6C(CO)16](2-) structure, also a Co6 trigonal prism with one of the vertical edges bridged by two CO groups and the remaining eight edges each bridged by a single CO group. However, this [Co6C(CO)16](2-) structure is thermodynamically unstable with respect to CO loss reverting to the stable trigonal prismatic [Co6C(CO)15](2-). This suggests that 15 carbonyl groups is the maximum that can be attached to a Co6C skeleton in a stable compound. The lowest energy structure of [Co6C(CO)14](2-) has a highly distorted octahedral Co6 skeleton and is thermodynamically unstable with respect to disproportionation to [Co6C(CO)15](2-) and [Co6C(CO)13](2-). The lowest energy [Co6C(CO)13](2-) structure is very similar to a known stable structure with an octahedral Co6 skeleton. The lowest energy [Co6C(CO)12](2-) structure is a relatively symmetrical D3d structure containing a carbon-centered Co6 puckered hexagon in the chair form.     

Synthesis and structure of boron-bridged constrained geometry complexes of titanium

The boron-bridged constrained geometry titanium complexes [Ti[eta5:eta1-(C5H4)B(NR2)NPh](NMe2)2][R = iPr (3), SiMe3(4)] and [Ti[eta5:eta1-(C9H6)B(NiPr2)NPh](NMe2)2](12) have been prepared in good yields by amine elimination reaction from [Ti(NMe2)4]. Subsequent deamination-chlorination with excess Me3SiCl yielded the corresponding dichloro-complexes (5, 6, 13). Reaction of the analogous ligand precursors (C5H5)B(NiPr2)N(H)R (R = Cy, tBu) with [Ti(NMe2)4] did not result in the expected bridged compounds, but rather in the half-sandwich complexes [Ti[(eta5-C5H4)B(NiPr2)N(H)R](NMe2)3][R = Cy (9), tBu (10)]. All compounds were fully characterised by means of multinuclear NMR spectroscopy. Thorough investigation of substituent effects was achieved by comparative X-ray diffraction studies on complexes 3, 5, 6 and 12.     

Characterization of acylphosphatidylglycerols from <Emphasis Type="Italic">salmonella typhimurium</Emphasis> by tandem mass spectrometry with electrospray ionization

Acylphosphatidylglycerol (Acyl-PG), a polar lipid class containing three fatty acyl groups, was isolated from Salmonella bacteria and characterized by tandem quadrupole and quadrupole ion-trap mass spectrometric methods with electrospray ionization. The structural characterization of the acyl-PG with various acyl groups (A-B/C-PG, where A not equal B not equal C) is based on the findings that the carboxylate anions (R(x)CO(2)(-)) arising from sn-2 (R(2)CO(2)(-)) is more abundant than that arising from sn-3' (R(3')CO(2)(-)), which is much more abundant than that arising from sn-1 (R(1)CO(2)(-)). This information provides a simple method for determination of the fatty acyl moieties and their positions in the molecule. The structural identification of the molecule can also be achieved by the findings that the fragment ion reflecting the ketene loss at sn-2 is more prominent than that reflecting the acid loss (i.e., [M - H - R'(2)CH=CO](-) > [M - H - R(2)CO(2)H](-)), while the ion arising from acid loss at sn-1 or sn-3' is, respectively, more abundant than the corresponding ketene loss (i.e., [M - H - R(1)CO(2)H](-) > [M - H - R'(1)CH=CO](-); [M - H - R(3')CO(2)H](-) > [M - H -R'(3')CH=CO](-)). The identity of the acyl moiety at sn-3' can be confirmed by an acyl-glycerophosphate anion observed in the product-ion spectrum obtained with a triple-stage quadrupole (TSQ) instrument, but not in that obtained with an ion-trap mass spectrometer (ITMS). However, the MS(2)-spectrum obtained with an ITMS is featured by the ion series that abundances of [M - H - R'(2)CH=CO - R(3)CO(2)H - 74](-) > [M - H - R'(2)CH=CO - R(1)CO(2)H - 74](-) z.Gt; [M - H - R'(1(or 3'))CH=CO - R(3'(or 1))CO(2)H - 74](-). This information also facilitates structural elucidation of the acyl-PG subclass that contains various acyl substituents. Structural identifications of molecular species having two identical fatty acyl substituents at sn-1, sn-2, or sn-3' or consisting of more than one isomeric structures are also demonstrated. The identities of the minor isomeric species in the molecules can be revealed by the aforementioned structural information arising from the various ion series combined.     

Atropisomeric (R,R)-2,2'-Bi([2]paracyclo[2](5,8)quinolinophane) and (R,R)-1,1'-Bi([2]paracyclo[2](5,8)isoquinolinophane): synthesis, structural analysis, and chiroptical properties

Atropisomeric (R,R)-2,2'-bi([2]paracyclo[2](5,8)quinolinophane) [(R,R)-1] and (R,R)-1,1'-bi([2]paracyclo[2](5,8)isoquinolinophane) [(R,R)-2] have been prepared in moderate overall yield (17 and 9%, respectively) by a four-step sequence starting from (R)-(-)-4-amino[2.2]paracyclophane and (R)-(-)-4-carboxy[2.2]paracyclophane, respectively. The structures have been determined on the basis of NOE (1)H NMR analysis and molecular mechanics (MM) calculations performed with a Spartan02 program, using the MMF94s force field. A preliminary, qualitative analysis of the chiroptical properties of these two compounds has also been attempted. The main spectral data can be interpreted in terms of an almost planar 2,2'-bisquinoline chromophore inserted in a paracyclophane structure in the case of (R,R)-1, while in the case of (R,R)-2, the main role is played by a distorted 1,1'-bisisoquinoline chromophore. On the basis of the above structural results, a hypothesis about the enantioselection capability of these two molecules has also been formulated.     

Reactions of [Et(4)N](3)[Sb{Fe(CO)(4)}(4)] with Alkyl Halides and Dihalides: Formation of the Alkyl- and the Dialkylantimony-Iron Carbonyl Complexes

The reactions of [Et(4)N](3)[Sb{Fe(CO)(4)}(4)] (1) with RX (R = Me, Et, n-Pr; X = I) in MeCN form the monoalkylated antimony complexes [Et(4)N](2)[RSb{Fe(CO)(4)}(3)] (R = Me, 2; R = Et, 4; R = n-Pr, 6) and the dialkylated antimony clusters [Et(4)N][R(2)Sb{Fe(CO)(4)}(2)] (R = Me, 3; R = Et, 5; R = n-Pr, 7), respectively. When [Et(4)N](3)[Sb{Fe(CO)(4)}(4)] reacts with i-PrI, only the monoalkylated antimony complex [Et(4)N](2)[i-PrSb{Fe(CO)(4)}(3)] (8) is obtained. The mixed dialkylantimony complex [Et(4)N][MeEtSb{Fe(CO)(4)}(2)] (9) also can be synthesized from the reaction of 2 with EtI. While the reaction with Br(CH(2))(2)Br produces [Et(4)N](2)[BrSb{Fe(CO)(4)}(3)] (10), treatment with Cl(CH(2))(3)Br forms the monoalkylated product [Et(4)N](2)[Cl(CH(2))(3)Sb{Fe(CO)(4)}(3)] (11) and a dialkylated novel antimony-iron complex [Et(4)N][{&mgr;-(CH(2))(3)}Sb{Fe(CO)(4)}(3)] (12). On the other hand, the reaction with Br(CH(2))(4)Br forms the monoalkylated antimony product and the dialkylated antimony complex [Et(4)N][{&mgr;-(CH(2))(4)}Sb{Fe(CO)(4)}(2)] (13). Complexes 2-13 are characterized by spectroscopic methods or/and X-ray analyses. On the basis of these analyses, the core of the monoalkyl clusters consists of a central antimony atom tetrahedrally bonded to one alkyl group and three Fe(CO)(4) fragments and the dialkyl products are structurally similar to the monoalkyl clusters, with the central antimony bonded to two alkyl groups and two Fe(CO)(4) moieties in each case. The dialkyl complex 3 crystallizes in the monoclinic space group P2(1)/c with a = 13.014(8) ?, b = 11.527(8) ?, c = 17.085(5) ?, beta = 105.04(3) degrees, V = 2475(2) ?(3), and Z = 4. Crystals of 12 are orthorhombic, of space group Pbca, with a = 14.791(4) ?, b = 15.555(4) ?, c = 27.118(8) ?, V = 6239(3) ?(3), and Z = 8. The anion of cluster 12 exhibits a central antimony atom bonded to three Fe(CO)(4) fragments with a -(CH(2))(3)- group bridging between the Sb atom and one Fe(CO)(4) fragment. This paper discusses the details of the reactions of [Et(4)N](3)[Sb{Fe(CO)(4)}(4)] with a series of alkyl halides and dihalides. These reactions basically proceed via a novel double-alkylation pathway, and this facile methodology can as well provide a convenient route to a series of alkylated antimony-iron carbonyl clusters.     

Structural characterization of phosphatidyl-<Emphasis Type="Italic">myo</Emphasis>-inositol mannosides from <Emphasis Type="Italic">Mycobacterium bovis</Emphasis> bacillus calmette guérin by multiple-stage quadrupole ion-trap mass spectrometry with electrospray ionization. I. PIMs and lyso-PIMs

We described a multiple-stage ion-trap mass spectrometric approach to characterize the structures of phosphatidylinositol and phosphatidyl-myoinositol mannosides (PIMs) in a complex mixture isolated from Mycobacterium bovis Bacillus Calmette Guérin. The positions of the fatty acyl substituents of PIMs at the glycerol backbone can be easily assigned, based on the findings that the ions arising from losses of the fatty acid substituent at sn-2 as molecules of acid and of ketene, respectively (that is, the [M - H - R(2)CO(2)H](-) and [M - H - R(2)CHCO](-) ions), are respectively more abundant than the ions arising from the analogous losses at sn-1 (that is, the [M - H - R(1)CO(2)H](-) and [M - H - R(1)CHCO](-) ions) in the MS(2) product-ion spectra of the [M - H](-) ions desorbed by electrospray ionization (ESI). Further dissociation of the [M - H - R(2)CO(2)H](-) and [M - H - R(1)CO(2)H](-) ions gives rise to a pair of unique ions corresponding to losses of 74 and 56 Da (that is, [M - H - R(x)CO(2)H - 56](-) and [M - H - R(x)CO(2)H - 74](-) ions, x = 1, 2), respectively, probably arising from various losses of the glycerol. The profile of the ion-pair in the MS(3) spectrum of the [M - H - R(2)CO(2)H](-) ion is readily distinguishable from that in the MS(3) spectrum of the [M - H - R(1)CO(2)H](-) ion and thus the assignment of the fatty acid substituents at the glycerol backbone can be confirmed. The product-ion spectra of the [M - H](-) ions from 2-lyso-PIM and from 1-lyso-PIM are discernible and both spectra contain a unique ion that arises from primary loss of the fatty acid substituent at the glycerol backbone, followed by loss of a bicyclic glycerophosphate ester moiety of 136 Da. The combined structural information from the MS(2) and MS(3) product-ion spectra permit the complex structures of PIMs that consist of various isomers to be unveiled in detail.     

Second-order Møller-Plesset theory with linear R12 terms (MP2-R12) revisited: auxiliary basis set method and massively parallel implementation

Ab initio electronic structure approaches in which electron correlation explicitly appears have been the subject of much recent interest. Because these methods accelerate the rate of convergence of the energy and properties with respect to the size of the one-particle basis set, they promise to make accuracies of better than 1 kcal/mol computationally feasible for larger chemical systems than can be treated at present with such accuracy. The linear R12 methods of Kutzelnigg and co-workers are currently the most practical means to include explicit electron correlation. However, the application of such methods to systems of chemical interest faces severe challenges, most importantly, the still steep computational cost of such methods. Here we describe an implementation of the second-order M?ller-Plesset method with terms linear in the interelectronic distances (MP2-R12) which has a reduced computational cost due to the use of two basis sets. The use of two basis sets in MP2-R12 theory was first investigated recently by Klopper and Samson and is known as the auxiliary basis set (ABS) approach. One of the basis sets is used to describe the orbitals and another, the auxiliary basis set, is used for approximating matrix elements occurring in the exact MP2-R12 theory. We further extend the applicability of the approach by parallelizing all steps of the integral-direct MP2-R12 energy algorithm. We discuss several variants of the MP2-R12 method in the context of parallel execution and demonstrate that our implementation runs efficiently on a variety of distributed memory machines. Results of preliminary applications indicate that the two-basis (ABS) MP2-R12 approach cannot be used safely when small basis sets (such as augmented double- and triple-zeta correlation consistent basis sets) are utilized in the orbital expansion. Our results suggest that basis set reoptimization or further modifications of the explicitly correlated ansatz and/or standard approximations for matrix elements are necessary in order to make the MP2-R12 method sufficiently accurate when small orbital basis sets are used. The computer code is a part of the latest public release of Sandia's Massively Parallel Quantum Chemistry program available under GNU General Public License.     

Oligomeric rods of alkyl- and hydridogallium imides

Reaction of [RGa(NMe(2))(2)](2), where R = Me, Et, Bu, and Hx, with ammonia at 150 degrees C in an autoclave produced insoluble white powders formulated as oligomers of [RGaNH](n). The analogous reaction between NH(3) and MeGa[N(SiMe(3))(2)](2) at low temperature (<25 degrees C) formed an isolable intermediate, [MeGa(mu-NH(2))N(SiMe(3))(2)](2), that was characterized using single-crystal X-ray diffraction. Infrared spectroscopy and X-ray diffraction of the oligomers were consistent with a rodlike structure comprised of six-membered, [RGaNH](3) rings stacked perpendicular to the long axis of the rod. The method of synthesis, formula, and diffraction results suggested a structural similarity between the alkyl, [RGaNH](n)(), and the previously reported hydride, [HGaNH](n). The structural and electronic properties of rods having the general formula H(3)[(HXYH)(3)](n)H(3) (XY = GaN, GeC; n = 1-9) were investigated using density functional theory. Atomic electronegativity differences between the group 13/15 and 14/14 systems were found to play important roles in the geometrical structures of the two rods and also caused significant differences in the electronic structures. Energetically, it was found to be increasingly favorable to add additional cyclotrigallazane rings to the GaN rods, while for the GeC rods, there was a roughly constant energy cost associated with each additional ring. The electric dipole moments of the GaN rods increased substantially with length; in the GeC rods, charge separation occurred to a much smaller extent and had a polarization opposite to that found in GaN. In addition, increased dipole moments correlated with smaller electronic excitation energies, as predicted by time-dependent density functional theory. All of the powders exhibited luminescence in the visible spectrum at room temperature. Structure observed in the photoluminescence spectra of [HGaNH](n) and [MeGaNH](n) was interpreted as arising from rods of different length.