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We report further investigations to aid the development of a Laplace MP2 (second-order Møller Plesset) method with a range separated Coulomb potential partitioned into short- and long-range parts. The implementation of the method extensively uses sparse matrix algebra, density fitting techniques for the short-range part, and a Fourier transformation in spherical coordinates for the long-range part of the potential. Localized molecular orbitals are employed for the occupied space, whereas virtual space is described by orbital specific virtual orbitals (OSVs) associated with localized molecular orbitals. The Fourier transform is deficient for very large distances between localized occupied orbitals, and a multipole expansion for widely separated pairs is introduced for the direct MP2 contribution, which is applicable also to non-Coulombic potentials that do not satisfy the Laplace equation. For the exchange contribution, an efficient screening of contributing localized occupied pairs is employed, which is discussed more completely here. To mitigate errors due to the truncation of OSVs, a simple and efficient extrapolation procedure is used to obtain results close to MP2 for the full basis set of atomic orbitals Using a suitable set of default parameters, the accuracy of the approach is demonstrated. The current implementation of the approach is not very efficient, and the aim of this paper is to introduce and critically discuss ideas that can have more general applicability beyond MP2 calculations for large molecules.

We report the development of a new Laplace MP2 (second-order Moller–Plesset) implementation using a range separated Coulomb potential, partitioned into short- and long-range parts. The implementation heavily relies on the use of sparse matrix algebra, density fitting techniques for the short-range Coulomb interactions, while a Fourier transformation in spherical coordinates is used for the long-range part of the potential. Localized molecular orbitals are employed for the occupied space, whereas orbital specific virtual orbitals associated with localized molecular orbitals are obtained from the exchange matrix associated with specific localized occupied orbitals. The range separated potential is crucial to achieve efficient treatment of the direct term in the MP2, while extensive screening is employed to reduce the expense of the exchange contribution in MP2. The focus of this paper is on controllable accuracy and linear scaling of the data entering the algorithm.

Density functional theory (DFT) calculations and infrared multiple photon dissociation (IRMPD) spectroscopy are employed to probe [TM·(B12H12)]− and [TM·(B12H12)2]2– clusters [TM = Ag(I), Cu(I), Co(II), Ni(II), Zn(II), Cd(II)]. A comparison is made between the charge-transfer properties of the clusters containing the hydrogenated dodecaborate dianions, B12H122–, and the fluorinated analogues, B12F122–, for clusters containing Cd(II), Co(II), Ni(II), and Zn(II). IRMPD of the [TM·(B12H12)]− and [TM·(B12H12)2]2– species yields B12H11– via hydride abstraction and B12H12– in all cases. To further explore the IR-induced charge-transfer properties of the B12X122– (X = H, F) cages, mixed-cage [TM(B12H12)(B12F12)]2– [TM = Co(II), Ni(II), Zn(II), Cd(II)] clusters were investigated. IRMPD of the mixed-cage species yielded appreciable amounts of B12F12– and B12H12– in most cases, indicating that charge-transfer to the central TM cation is a favorable process; formation of B12F12– is the dominant process for the Co(II...

International audience; G-quadruplexes (G4s) have become important drug targets to regulate gene expression and telomere maintenance. Many studies on G4 ligand binding focus on determining the ligand binding affinities and selectivities. Ligands, however, can also affect the G4 conformation. Here we explain how to use electrospray ionization mass spectrometry (ESI-MS) to monitor simultaneously ligand binding and cation binding stoichiometries. The changes in potassium binding stoichiometry upon ligand binding hint at ligand-induced conformational changes involving a modification of the number of G-quartets. We investigated the interaction of three quadruplex ligands (PhenDC3, 360A and Pyridostatin) with a variety of G4s. Electrospray mass spectrometry makes it easy to detect K+ displacement (interpreted as quartet disruption) upon ligand binding, and to determine how many ligand molecules must be bound for the quartet opening to occur. The reasons for ligand-induced conversion to antiparallel structures with fewer quartets are discussed. Conversely, K+ intake (hence quartet formation) was detected upon ligand binding to G-rich sequences that did not form quadruplexes in 1 mM K+ alone. This demonstrates the value of mass spectrometry for assessing not only ligand binding, but also ligand-induced rearrangements in the target sequence. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.

The preferential solvation behavior for eight different derivatives of protonated quinoline was measured in a tandem differential mobility spectrometer mass spectrometer (DMS-MS). Ion-solvent cluster formation was induced in the DMS by the addition of chemical modifiers (i.e., solvent vapors) to the N2 buffer gas. To determine the effect of more than one modifier in the DMS environment, we performed DMS experiments with varying mixtures of water, acetonitrile, and isopropyl alcohol solvent vapors. The results show that doping the buffer gas with a binary mixture of modifiers leads to the ions binding preferentially to one modifier over another. We used density functional theory to calculate the ion-solvent binding energies, and in all cases, calculations show that the quinolinium ions bind most strongly with acetonitrile, then isopropyl alcohol, and most weakly with water. Computational results support the hypothesis that the quinolinium ions bind exclusively to whichever solvent they have the strongest interaction with, regardless of the presence of other modifier gases.

Clusters of all-cis 1,2,3,4,5,6-hexafluorocyclohexane and the dodecafluorododecaboron dianion, [C6F6H6]n[B12F12]2– (n = 0–4), are investigated in a combined experimental and computational study. DFT calculations and IRMPD spectra in the region of 800–2000 cm–1 indicate that C6H6F6 binds to open trigonal faces of B12F122– via a three-point interlocking binding motif. Calculated binding interactions reveal substantial contributions from C–H···F hydrogen bonding and binding energies that are among the strongest observed for a neutral-anion system.

Infrared multiple photon dissociation spectra of the proton-bound heterodimers of phenylalanine/glycine (Phe·H + ·Gly) and pentafluorophenylalanine/glycine (F 5 -Phe·H + ·Gly) have been acquired in the 975–1975 cm −1 region. Exhaustive basin hopping molecular dynamics searches and subsequent DFT calculations predict four low energy intermolecular binding motifs. The spectrum of F 5 -Phe·H + ·Gly is assigned predominantly to isomers exhibiting a N H + ⋯O intermolecular interaction between nitrogen-protonated Gly and the carbonyl oxygen atom of F 5 -Phe. In contrast, the spectrum Phe·H + ·Gly is found to consist of a mixture of isomers exhibiting the N H + ⋯O between nitrogen-protonated Gly and the carbonyl oxygen of neutral Phe, and isomers exhibiting a N H + ⋯N interaction between nitrogen-protonated Phe and the neutral Gly moiety. Cation-π effects also seem to influence the cluster geometries, especially in the case of the Phe·H + ·Gly global minimum structure where the phenyl ring orients with the site of protonation so as to maximize charge-quadrupole interactions.

Density functional theory (DFT) calculations and infrared multiple photon dissociation (IRMPD) spectroscopy are employed to probe [TM·(B

It is generally assumed that molecules behave ergodically during chemical reactions, that is, reactivities depend only on the total energy content and not on the initial state of the molecule. While there are a few examples of nonergodic behavior in small (usually electronically excited) species, to date there have been no reports of such behavior in larger covalently bound species composed of several tens of atoms. Here, we demonstrate vibrational mode-selective behavior in a series of palladium catalysts. When we excite solvent-tagged gas-phase Pd catalysts with an infrared laser that is tuned to be resonant with specific molecular vibrations, depending on which vibration we excite, we can select different reaction pathways. We also demonstrate that this behavior can be “turned off” via chemical substitution.

Clusters of all-cis 1,2,3,4,5,6-hexafluorocyclohexane and the dodecafluorododecaboron dianion, [C

The structures and properties of a series of phenylalanine (Phe) derivatives have been investigated in a joint computational and experimental infrared multiple photon dissociation (IRMPD) study. IRMPD spectra in the 1000–2000 cm−1 region show that protonation is localized on the amine group in all cases. Intramolecular cation–π interactions between the ammonium group and the phenyl ring heavily influence molecular geometries and properties such as gas phase basicity and proton affinity. By varying substituents on the phenyl ring, one can sensitively tune the cation–π interaction and, therefore, the molecular structure and properties. Variations in molecular structures and properties as a function of phenyl ring substitution are shown to correlate with substituent Hammett parameters.

Hypercoordinated complexes involving tricarbastannatrane cation [N(CH2CH2CH2)3Sn]+ with various Lewis bases are investigated in the gas and solution phases using a combination of infrared multiple photon dissociation (IRMPD) spectroscopy, NMR spectroscopy, and density functional theory calculations. Coordination is found to occur at the apical position leading to a pentacoordinated Sn center. Strongly electron donating Lewis bases disrupt the N···Sn transannular interaction and induce higher degrees of geometric distortion at the metal center than weakly donating Lewis bases, an effect that manifests as anharmonic shifts in the vibrational spectra. Once characterized in the gas phase, [N(CH2CH2CH2)3Sn(Lewis base)]+ structures were embedded in a dichloroethane polarizable continuum model to investigate solution phase properties. Calculated 119Sn NMR chemical shifts were found to be in good agreement with those measured experimentally, thus suggesting that the bonding properties of [N(CH2CH2CH2)3Sn]+ are es...

The authors acknowledge support in the form of NSERC (Canada) Discovery Grants to EF, WSH, and TBM and an EPSRC (UK) responsive mode grant to DO’H and NSK is gratefully acknowledged. Experiments have been carried out in which electrospray ionization has been used to generate ionic complexes of all-cis 1,2,3,4,5,6 hexafluorocyclohexane. These complexes were subsequently mass isolated in a quadrupole ion trap mass spectrometer and then irradiated by the tunable infrared output of a free electron laser in the 800-1600 cm−1 range. From the frequency dependence of the fragmentation of the complexes, vibrational signatures of the complexes were obtained. Computational work carried out in parallel reveals that the complexes formed are very strongly bound and are among the most strongly bound complexes of Na+ and Cl− ever observed with molecular species. The dipole moment calculated for the heaxafluorocyclohexane is very large (~7 D) and it appears that the bonding in each of the complexes has a significant electrostatic contribution. Postprint

A basin-hopping search strategy has been used to determine likely candidates for low-energy Rh(n)S(0,±) (n = 1-9) cluster structures. Cluster structures were optimized at the density functional level of theory using the PBE and PBE0 functionals. Ionization energies, electron detachment energies, HOMO-LUMO gap energies, UV-visible spectra, low-lying fragmentation channels and energies, cluster structures, spin multiplicities, and vibrational spectra are predicted for Rh(n)S(0,±) and Rh(n+1)(0,±) (n = 1-9). Donation from valence sulfur atomic p orbitals to valence rhodium atomic d orbitals and back-donation to valence sulfur atomic d orbitals leads to electron density delocalization and metal-like behavior for rhodium sulfide clusters.