Density matrix averaged atomic natural orbital (ANO) basis sets for correlated molecular wave functions

Summary Generally contracted basis sets for first row atoms have been constructed using the Atomic Natural Orbital (ANO) approach, with modifications for allowing symmetry breaking and state averaging. The ANOs are constructed by averaging over several atomic states, positive and negative ions, and atoms in an external electric field. The contracted basis sets give virtually identical results as the corresponding uncontracted sets for the atomic properties, which they have been designed to reproduce. The design objective has been to describe the ionization potential, the electron affinity, and the polarizability as accurately as possible. The result is a set of well-balanced basis sets for molecular calculations. The starting primitive sets are 8s4p3d for hydrogen, 9s4p3d for helium, and 14s9p4d3f for the heavier first row atoms.     

Mode locking a 1550 nm semiconductor disk laser by using a GaInNAs saturable absorber

Passive mode locking of an optically pumped, InP-based, 1550 nm semiconductor disk laser by using a GaInNAs saturable absorber mirror is demonstrated. To reduce material heating and enable high-power operation, a 50 microm thick diamond heat spreader is bonded to the surface of the gain chip. The laser operates at a repetition frequency of 2.97 GHz and emits near-transform-limited 3.2 ps pulses with an average output power of 120 mW.     

Molecular dynamics simulations of the interactions between platinum clusters and carbon platelets

Molecular dynamics simulations have been performed with two reactive force fields to investigate the structure of a Pt100 cluster adsorbed on the three distinct sides of a carbon platelet. A revised Reax force field for the carbon-platinum system is presented. In the simulations, carbon platelet edges both with and without hydrogen termination have been studied. It is found that the initial mismatch between the atomic structure of the platelet egde and the adsorbed face of the Pt100 cluster leads to a desorption of a few platinum atoms from the cluster and the subsequent restructuring of the cluster. Consequently, the average Pt-Pt bond length is enlarged in agreement with experimental results. This change in the bond length is supposed to play an important role in the enhancement of the catalytic activity, which is demonstrated by studying the changes in the bond order of the platinum atoms. We found an overall shift to lower values as well as a loss of the well-defined peak structure in the bond-order distribution.     

Plasmid purification using non-porous anion-exchange silica fibres

A new type of fibre-based anion-exchange material for plasmid purification was developed. The basic material consisted of non-porous silica fibres with a mean diameter of 1.5 microm and a surface area of 2.4m(2)g(-1). The fibre surface was provided with several types of ligands, either by adsorption of polymers (chitosan or poly(ethyleneimine)) or by polymerization of amine-containing acrylic monomers onto a propyl methacrylate-silanized surface. The resulting polymer layers contained primary, tertiary or quaternary amines as ion-exchange groups. The packing density could be varied considerably, 9-34% (v/v). The loose packing structure provided excellent flow properties suitable for high-speed operations. The best overall performance was shown by silica fibres provided with tertiary amine polymers, having a plasmid-binding capacity of 0.9 mg ml(-1) (pre-purified plasmid) and a plasmid recovery of 62% (performance data remained stable though several adsorption cycles). The high flow rates possible with the fibre material made it especially useful when large volumes of cleared lysate were processed. The columns could be operated with retention of their adsorption properties at speeds of up to 1800 cm h(-1), equivalent to 0.5 column volumes per minute. The binding capacity was found to be lower than anticipated from the design of the fibres. Fluorescence imaging showing individual plasmid molecules indicated the fibre population to be heterogeneous with respect to plasmid adsorption, some fibres displaying poor binding properties. Possible reasons for this heterogeneity are discussed.     

High-capacity composite adsorbents for nucleic acids

Cytopore™ is a bead-shaped, macroporous and easily compressible cellulose-based anion-exchange material intended for cultivation of anchor-dependent animal cells. Reticulated vitreous carbon (RVC) is a strong, non-compressible, high voidage (97%) matrix material that can be cut to desired geometrical shapes. Cytopore and RVC were combined to cylindrical composites (25 mm × 10 mm) fitted inside chromatography columns. The composite combined the advantageous properties of both its constituents, making it suitable for column chromatography. The composite could withstand very high flow rates without compaction of the bed (>25 column volumes/min; 4000 cm h⁻¹). Chromatography runs with tracers showed a low HETP value (0.3 mm), suggesting that pore flow was in operation. The dynamic binding capacities (10% breakthrough) per gram of dry weight Cytopore were determined for several compounds including DNA and RNA and were found to be 240–370 mg/g. The composite was used to isolate pUC 18-type plasmids from a cleared alkaline lysate in a good yield. Confocal microscopy studies showed that plasmids were bound not only to the surface of the Cytopore material but also within the matrix walls, thus offering an explanation to the very high binding capacities observed. The concept of using a composite prepared from a mechanically weak, high-binding material and a strong scaffold material may be applied to other systems as well.     

Extensive NMRD studies of Ni(II) salt solutions in water and water-glycerol mixtures

Aqueous solutions of simple nickel(II) salts are a classical test case for theories of the paramagnetic relaxation enhancement (PRE) and its dependence on the magnetic field (nuclear magnetic relaxation dispersion, NMRD), going back to late fifties. We present here new experimental data, extending the NMRD range up to 21T (900 MHz). In addition to salt solutions in (acidified) water, we have also measured on solutions containing glycerol. The aqueous solution data do not show any significant changes compared to the earlier experiments. The interpretation, based on the general ("slow-motion") theory is also similar to the earlier work from our laboratory. The NMRD-data in mixed solvents are qualitatively different, indicating that the glycerol not only changes the solution viscosity, but may also enter the first coordination sphere of the metal ion, resulting in lower symmetry complexes, characterized by non-vanishing averaged zero-field splitting. This hypothesis is corroborated by molecular dynamics simulations. A strategy appropriate for interpreting the NMRD-data for the chemically complicated systems of this type is proposed.     

The inclusion of electron correlation in intermolecular potentials: applications to the formamide dimer and liquid formamide

A test of the quality of the electrostatic properties and polarizabilities used in the nonempirical molecular orbital (NEMO) potential is carried out for formamide by calculating the molecular dipole moment and polarizability at the second-order M?ller–Plesset (MP2) level of theory. The molecular dipole moment is 11% lower at the MP2 level than at the Hartree–Fock (HF) level, whereas the isotropic part of the polarizability is increased by 36% by adding electron correlation and using a considerably larger basis set. The atomic charges, dipole moments and polarizabilities obtained at the HF level are rescaled to get the correct molecular properties at the MP2 level. The potential minimum for the cyclic dimer of formamide is −17.50 kcal/mol with the MP2-scaled properties and is significantly lower than other potentials give. Two intermolecular potentials are constructed and used in subsequent molecular dynamics simulations: one with the regular NEMO potential and the other with the rescaled MP2 properties. A damping of the electrostatic field at short intermolecular distances is included in the present NEMO model. The average energies for liquid formamide are lower for the MP2-scaled model and are in good agreement with experimental results. The lowering of the simulation energy for the MP2-scaled potential indicates the strong dispersive interactions in liquid formamide. Received: 20 March 2000 / Accepted: 18 April 2000 / Published online: 18 August 2000     

Influence of droplet size, capillary-cone distance and selected instrumental parameters for the analysis of noncovalent protein-ligand complexes by nano-electrospray ionization mass spectrometry

It has been suggested in the literature that nano-electrospray ionization (nano-ESI) mass spectrometry better reflects the equilibrium between complex and free protein in solution than pneumatically assisted electrospray ionization (ESI) in noncovalent interaction studies. However, no systematic studies of the effects of ionization conditions have been performed to support this statement. In the present work, different instrumental and sample-derived parameters affecting the stability of noncovalent complexes during analysis by nano-ESI were investigated. In general, increased values of parameters such as drying gas flow-rate, ion-source temperature, capillary tip voltage and buffer concentration lead to a dissociation of ribonuclease A (RNAse)-cytidine 2'-monophosphate (CMP) and cytidine 5'-triphosphate (CTP) complexes. The size of the electrosprayed droplets was shown to be an important issue. Increasing the capillary to cone distance yielded an increased complex to free protein ratio when a hydrophilic ligand was present and the reverse effect was obtained with a hydrophobic ligand. Important in this regard is the degree of sampling of ions originating from late-generation residue droplets, that is, ions present in the droplet bulk. Sampling of these ions increases with longer capillary-cone distance (flight time). Furthermore, when the sample flow-rate was increased by increasing the capillary internal tip i.d. from 4 to 30 microm, a decreased complex to free protein ratio for the RNAse-CTP system was observed. This behavior was consistent with the change in surface to volume ratio for flow-rates between 2 and 100 nl min(-1). Finally, polarity switching between positive and negative ion modes gave a higher complex to free protein ratio when the ligand and the protein had the same polarity.     

New relativistic ANO basis sets for transition metal atoms

New basis sets of the atomic natural orbital (ANO) type have been developed for the first, second, and third row transition metal atoms. The ANOs have been obtained from the average density matrix of the ground and lowest excited states of the atom, the positive and negative ions, and the atom in an electric field. Scalar relativistic effects are included through the use of a Douglas-Kroll-Hess Hamiltonian. Multiconfigurational wave functions have been used with dynamic correlation included using second order perturbation theory (CASSCF/CASPT2). The basis sets are applied in calculations of ionization energies, electron affinities, and excitation energies for all atoms and polarizabilities for spherically symmetric atoms. These calculations include spin-orbit coupling using a variation-perturbation approach. Computed ionization energies have an accuracy better than 0.2 eV in most cases. The accuracy of computed electron affinities is the same except in cases where the experimental values are smaller than 0.5 eV. Accurate results are obtained for the polarizabilities of atoms with spherical symmetry. Multiplet levels are presented for some of the third row transition metals.