Advances in methods and algorithms in a modern quantum chemistry program package

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.     

Vibrational spectroscopy for glycine adsorbed on silicon clusters: Harmonic and anharmonic calculations for models of the Si(1 0 0)-2 × 1 surface

The vibrational spectroscopy of a glycine molecule adsorbed on a silicon surface is studied computationally, using different clusters as models for the surface. Harmonic frequencies are computed using density functional theory (DFT) with the B3LYP functional. Anharmonic frequency calculations are carried out using vibrational self-consistent field (VSCF) algorithms on an improved PM3 potential energy surface. The results are compared with experiments on Glycine@Si(1 0 0)-2 × 1.

The main findings are: (1) Agreement of the computed frequencies with experiment improves with cluster size. (2) The anharmonic calculations are generally in better agreement with experiment than the harmonic ones. The improvements due to anharmonicity are most significant for hydrogenic stretching. (3) An important part of the anharmonic effects is due to anharmonic coupling between different normal modes of the system. (4) The anharmonic coupling between glycine vibrational modes is much larger than the anharmonic coupling between glycine and “phonon” (cluster) modes.

Implications of the results for surface vibrational spectroscopy are discussed.     

Anharmonic vibrational spectroscopy calculations with electronic structure potentials: comparison of MP2 and DFT for organic molecules

Density functional theory (DFT) technique is the most commonly used approach when it comes to computation of vibrational spectra of molecular species. In this study, we compare anharmonic spectra of several organic molecules such as allene, propyne, glycine, and imidazole, computed from ab initio MP2 potentials and DFT potentials based on commonly used BLYP and B3LYP functionals. Anharmonic spectra are obtained using the direct vibrational self-consistent field (VSCF) method and its correlation-corrected extension (CC-VSCF). The results of computations are compared with available experimental data. It is shown that the most accurate vibrational frequencies are obtained with the MP2 method, followed by the DFT/B3LYP method, while DFT/BLYP results are often unsatisfactory. Contribution to the Mark S. Gordon 65th Birthday Festschrift Issue.     

Conformational transitions of glycine induced by vibrational excitation of the O-H stretch

Vibrational energy flow and conformational transitions following excitation of the OH stretching mode of the most stable conformer of glycine are studied by classical trajectories. "On the fly" simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are selected to correspond to the ν=1 excitation of the OH stretch. The main findings are: (1) An an equilibrium-like ratio is established between the populations of the 3 lowest-lying conformers after about 10 picoseconds. (2) There is a high probability throughout the 150 ps of the simulations for finding the molecule in geometries far from the equilibrium structures of the lowest-energy conformers. (3) Energy from the initial excited OH (ν=1) stretch flows preferentially to 5 other vibrational modes, including the bending motion of the H atom. (4) RRK theory yields conformational transition rates that deviate substantially from the classical trajectory results. Possible implication of these results for vibrational energy flow and conformational transitions in small biological molecules are discussed.     

Crystallographic analysis of metal-ion binding to human ubiquitin

The metal-binding ability of human ubiquitin (hUb) towards a selection of biologically relevant metal ions and complexes has been probed. Different techniques have been used to obtain crystals suitable for crystallographic analysis. In the first type of experiments, crystals of hUb have been soaked in solutions containing copper(II) acetate and two metallodrugs, Zeise salt (K[PtCl(3)(η(2)-C(2)H(4))]·H(2)O) and cisplatin (cis-[PtCl(2)(NH(3))(2)]). The Zeise salt is used in a test for hepatitis, whereas cisplatin is one of the most powerful anticancer drugs in clinical use. The Zeise salt readily reacts with hUb crystals to afford an adduct with three platinum residues per protein molecule, Pt(3)-hUb. In contrast, copper(II) acetate and cisplatin were found to be unreactive for contact times up to one hour and to cause degradation of the hUb crystals for longer times. In the second type of experiments, hUb was cocrystallized with a solution of copper(II) or zinc(II) acetate or cisplatin. Zinc(II) acetate gives, at low metal-to-protein molar ratios (8:1), crystals containing one metal ion per three molecules of protein, Zn-hUb(3) (already reported in previous work), whereas at high metal-to-protein ratios (70:1) gives crystals containing three Zn(II) ions per protein molecule, Zn(3)-hUb. In contrast, once again, copper(II) acetate and cisplatin, even at low metal-to-protein ratios, do not give crystalline material. In the soaking experiment, the Zeise anion leads to simultaneous platination of His68, Met1, and Lys6. Present and previous results of cocrystallization experiments performed with Zn(II) and other Group 12 metal ions allow a comprehensive understanding of the metal-ion binding properties of hUb with His68 as the main anchoring site, followed by Met1 and carboxylic groups of Glu16, Glu18, Glu64, Asp21, and Asp32, to be reached. In the case of platinum, Lys6 can also be a binding site. The amount of bound metal ion, with respect to that of the protein, appears to be a relevant parameter influencing crystal packing.     

Quantitation of homoharringtonine in plasma by high-performance liquid chromatography with amperometric detection

A high-performance liquid chromatographic procedure was developed for the quantitation of homoharringtonine in plasma. Harringtonine was used as an internal standard, and 1 ml of sample was required. The single-step extraction with dichloromethane resulted in almost 100% recovery for homoharringtonine and harringtonine. Analysis was performed on a reversed-phase CN column with amperometric detection. Chromatography was completed in 12 min. At an oxidation potential of +1.0 V, the detection limit was 1 ng/ml at a signal-to-noise ratio of 2. The mean analytical recovery for homoharringtonine was 99.5%. The within-run precision and between-run precision were both less than 11%. The method is equally applicable for plasma or serum, and it has been demonstrated to be applicable for study of the pharmacokinetics of homoharringtonine in patients suffering from acute non-lymphocytic leukaemia.     

Electrons Mediate the Gas‐Phase Oxidation of Formic Acid with Ozone

Gas‐phase reactions of CO₃^.? with formic acid are studied using Fourier transform ion cyclotron resonance (FT‐ICR) mass spectrometry. Signal loss indicates the release of a free electron, with the formation of neutral reaction products. This is corroborated by adding traces of SF₆ to the reaction gas, which scavenges 38 % of the electrons. Quantum chemical calculations of the reaction potential energy surface provide a reaction path for the formation of neutral carbon dioxide and water as the thermochemically favored products. From the literature, it is known that free electrons in the troposphere attach to O₂, which in turn transfer the electron to O₃. O₃^.? reacts with CO₂ to form CO₃^.?. The reaction reported here formally closes the catalytic cycle for the oxidation of formic acid with ozone, catalyzed by free electrons.     

On the Ambiphilic Reactivity of Geometrically Constrained Phosphorus(III) and Arsenic(III) Compounds: Insights into Their Interaction with Ionic Substrates

The ambiphilic nature of geometrically constrained Group 15 complexes bearing the N,N‐bis(3,5‐di‐tert‐butyl‐2‐phenolate)amide pincer ligand (ONO^3?) is explored. Despite their differing reactivity towards nucleophilic substrates with polarised element–hydrogen bonds (e.g., NH₃), both the phosphorus(III), P(ONO) ( 1 a ), and arsenic(III), As(ONO) ( 1 b ), compounds exhibit similar reactivity towards charged nucleophiles and electrophiles. Reactions of 1 a and 1 b with KOtBu or KNPh₂ afford anionic complexes in which the nucleophilic anion associates with the pnictogen centre ([(tBuO)Pn(ONO)]^? (Pn=P ( 2 a ), As ( 2 b )) and [(Ph₂N)Pn(ONO)]^? (Pn=P ( 3 a ), As ( 3 b )). Compound 2 a can subsequently be reacted with a proton source or benzylbromide to afford the phosphorus(V) compounds (tBuO)HP(ONO) ( 4 a ) and (tBuO)BzP(ONO) ( 5 a ), respectively, whereas analogous arsenic(V) compounds are inaccessible. Electrophilic substrates, such as HOTf and MeOTf, preferentially associate with the nitrogen atom of the ligand backbone of both 1 a and 1 b , giving rise to cationic species that can be rationalised as either ammonium salts or as amine‐stabilised phosphenium or arsenium complexes ([Pn{ON(H)O}]⁺ (Pn=P ( 6 a ), As ( 6 b )) and [Pn{ON(Me)O}]⁺ (Pn=P ( 7 a ), As ( 7 b )). Reaction of 1 a with an acid bearing a nucleophilic counteranion (such as HCl) gives rise to a phosphorus(V) compound HPCl(ONO) ( 8 a ), whereas the analogous reaction with 1 b results in the addition of HCl across one of the As?O bonds to afford ClAs{(H)ONO} ( 8 b ). Functionalisation at both the pnictogen centre and the ligand backbone is also possible by reaction of 7 a / 7 b with KOtBu, which affords the neutral species (tBuO)Pn{ON(Me)O} (Pn=P ( 9 a ), As ( 9 b )). The ambiphilic reactivity of these geometrically constrained complexes allows some insight into the mechanism of reactivity of 1 a towards small molecules, such as ammonia and water.     

Structural Manipulation of Ruthenium(II) Polypyridine Nitrone Complexes to Generate Phosphorogenic Bioorthogonal Reagents for Selective Cellular Labeling

We report a new class of ruthenium(II) polypyridine complexes functionalized with a nitrone group as phosphorogenic bioorthogonal probes. These complexes were very weakly emissive owing to rapid C=N isomerization of the nitrone moiety, but exhibited significant emission enhancement upon strain‐promoted alkyne–nitrone cycloaddition (SPANC) reaction with bicyclo[6.1.0]nonyne (BCN)‐modified substrates. The modification of nitrone with a dicationic ruthenium(II) polypyridine unit at the α‐C‐position and a phenyl ring at the N‐position led to remarkably accelerated reaction kinetics, which are substantially greater (up to ≈278 fold) than those of other acyclic nitrone–BCN systems. Interestingly, the complexes achieved specific cell membrane/cytosol staining upon specific labeling of an exogenous substrate, BCN‐modified decane (BCN‐C10), in live cells. Importantly, the in situ generation of the more lipophilic isoxazoline adduct in the cytoplasm resulted in increased cytotoxicity, highlighting a novel approach to apply the SPANC labeling technique in drug activation.