Extended Basis Set Calculations Research Articles

Monocation-driven proton transfer relays within G protein-coupled receptors of the rhodopsin class and the GTP synthase mechanism

Proton relay mechanisms involving acidic residues sited 10–12 Å apart within a general hydrophobic environment of a G protein ternary complex are examined for potential ligand-activated proton transport. Extended basis set calculations on Arg-Asp, Lys-Asp, Arg-Cys, Lys-Cys and potential His-Asp interactions are intrinsically dominated by preferred neutral hydrogen bonded complexes over their ion pair form. The early concept of ‘membrane-delimited monocation transfer’ associated with the stimulant action of ligands is identified with a potential monocation channel operating through the ternary complex where the monocation provides the driving force for the set of relays, each relay producing simple Na + or K +/H + exchange. Under the influence of the cation the ligand, nor-adrenaline, in the β 1-adrenergic receptor is then seen to act as a shuttle between two relays involving aspartate residues on the receptor’s α-helices III and II and delivers two protons through two relays returning towards the periplasm as a catechol anion. A set of proton transfer relays are identified within the G protein-coupled receptor complex which will convey a proton some 56 Å from an aspartate residue on α-helix III to a glutamate residue at the G protein cytoplasmic interface. This residue at the base of the Gα α2-helix is identified as the candidate residue for phosphorylation by many regulatory G protein signalling [RGS] proteins and defines the phosphorylated residue which, on proton activation, can transfer its metaphosphate group to the GTP held within the Gα protein supporting a GTP synthase mechanism. The attachment of the Gαβγ heterotrimer to the β 1-adrenergic receptor based on the positioning of extended receptor α-helices V, VI and the N-terminal α-helix of the Gsα-adapted protein within opposing clefts of the Gαβγ heterotrimer was found accurate for development of the relay mechanisms for mammalian receptors. The proposed monocation channel pathway is X-ray based but the completion of the proton transfer relay at the G protein–receptor interface utilised the Gsα C-terminal acid group necessitating movement of four C-terminal residues from the Gα.GTPγS X-ray structure. The model may be applied to both mammalian- and bacteriorhodopsin provided that the initial large dipole theoretically developed within the rhodopsin on absorption allows ligand movement to align itself with the potential gradient across the membrane. The delivery of two protons in the case of bovine rhodopsin towards the cytoplasm and in bacteriorhodopsin towards the periplasm with the respective monocation-assisted movement as carbanions can be supported by the expected isomers formed by electron deficient ( trans) or electron rich ( cis) backbones of the highly polarizable rhodopsin due to σ bond hyperconjugation.

Vibrational spectrum of glycine molecule

The infrared and Raman spectra of glycine molecule has been studied in spectral region 400–4000 cm −1 in solid form as well as in water. The vibrational frequencies for the fundamental modes of the glycine in neutral and its zwitterionic form have also been calculated using AM1 semiempirical method as well as ab initio method with minimal basis set. The reliability of the minimal basis set and AM1 method with higher basis sets, for IR spectra of the neutral glycine conformers were examined. We find that the 6–21G basis set calculation yields structural parameters, rotational constant and dipole moment of glycine conformers, which are very similar to those obtained from extended basis set calculation as well as experimental values. IR frequencies for glycine conformer I are also calculated in water using SCRF = PCM model and compared with experimental values. A comparison between calculated frequencies for neutral glycine, and its zwitterionic form with observed IR and Raman bands have been made. The total energies for gas phase glycine and its zwitterionic form along with those of hydrated forms were also calculated. It is found from the calculations that in the gas phase neutral glycine is more stable as compared to its zwitterionic form.

Performance of the Harris functional for extended basis sets at the Hartree-Fock and density functional levels.

The Harris functional is a noniterative variational procedure that uses an input charge density to produce an energy that is surprisingly accurate compared to the converged Kohn-Sham self-consistent result. We adapted and generalized this functional for the Hartree-Fock closed- and open-shell cases as well as examined its use for hybrid density functional methods such as B3LYP. Analysis of extended basis set calculations shows that at the B3LYP level an input density formed from a double zeta + polarization orbital basis is accurate enough to reproduce the energy of triple zeta + double polarization + diffuse orbital basis. For large molecules this translates into a computational speed that can be an order of magnitude faster. In the case of Hartree-Fock calculations a "bootstrapping technique" that employs successive applications of the Harris functional can further reduce computational times while retaining sufficient accuracy.

New theoretical insight into the thermal cis–trans isomerization of azo compounds: Protonation lowers the activation barrier

The detailed mechanism of thermal cis–trans inversion of protonated diazenes and azobenzenes has been investigated for the first time using ab initio Hartree–Fock (HF), density functional theory (DFT), second order Mo/ller–Plesset (MP2), and complete active space self consistent field (CASSCF) approaches. Protonation of one of the nitrogens at the N=N bond leads to a considerable (5–20 kcal/mol) reduction of the activation barrier. The magnitude of this effect depends on the electron withdrawing nature of the substituents and the differential stabilization of the transition state by positively charged functional groups. In the case of 4-phenylazopirydine protonated at pyridine nitrogen, the barrier is dramatically reduced to just 7 kcal/mol. This result establishes the lowest (close to an experimental estimate) ab initio value for the cis–trans isomerization for a substituted azobenzene. The structures of neutral and protonated transition states are similar, and the correlation effects for molecular parameters as well as the energy are negligible for extended basis set calculations.

Theoretical Modeling of the Hydrogen Abstraction Reaction of Fluoromethane by the Hydroxyl Radical

We have performed theoretical modeling of the reaction rate constants of the hydrogen abstraction reaction of fluoromethane (CH3F) by the hydroxyl radical (OH) using dual-level variational transition state theory calculation including multidimensional tunneling corrections from 200 to 1000 K. Correlated electronic structure theory with extended basis set calculation was applied for both the low-level reaction-path and the high-level stationary-point calculation. An improved interpolated correction scheme was used for better estimating the width of energy barrier by performing an intermediate-level electronic structure calculation. The calculated rate constants are in good agreement with available experimental values at most temperatures. The hydrogen kinetic isotope effects (KIEs) were also evaluated and analyzed. The current study suggested that the reaction has a relatively wide barrier, and the tunneling effects are thus not very important even at low temperatures. The current study also showed that th...

Barrier for the H2CO→H2+CO reaction: A discrepancy between high-level electronic structure calculations and experiment

The unimolecular dissociation of formaldehyde to H2+CO was studied using extended basis set calculations and a variety of medium-to-high accuracy correlation recovery techniques. These included second and fourth order perturbation theory, multireference configuration interaction wave functions, coupled cluster theory with perturbative triples and full iterative triples, and estimated full configuration interaction wave functions. The intrinsic error of the electronic structure methods was assessed by extrapolating total energies to the complete basis set limit. Our best estimate of the barrier height, including zero point vibrational effects, is 81.9±0.3 kcal/mol, almost 3 kcal/mol larger than the experimental value of 79.2±0.8 kcal/mol. This estimate includes corrections for the effects of finite basis set truncation (which is negligible at the quintuple zeta level), higher order correlation recovery, core/valence correlation, and scalar relativistic effects. Using the same theoretical approach, we estimate the exothermicity of the dissociation reaction to be −1.6 kcal/mol, compared to experimental values in the −0.4 to −2.2 kcal/mol range. New calculations of the unimolecular dissociation rate constants using a variety of techniques failed to reconcile theory and experiment.

Theoretical Investigation of the Second and Third Order Nonlinear Optical Properties of Some Fused Heterocyclic Aromatic Compounds

ABSTRACTWe report herein the results of coupled perturbed Hartree-Fock (CPHF) ab initio extended basis set calculations on the geometric structures, dipole moments, static first-order (α), second-order (β), and third-order polarizabilities (λ) of a series of fused heterocyclic aromatic compounds based on quinoline. The effects of the presence/absence of the heteroatom as well as the introduction of other substituents at various positions in the ring system on these molecular properties are described. The effect of the presence of N-oxide is also examined. Suggestions for the design of heterocyclic systems with enhanced polarizabilities are made.

Flexing analysis of steric exchange repulsion accompanying ethane internal rotation

Relaxation calculations using natural bond orbitals are carried out for the Puali exchange steric repulsion changes associated with ethane internal rotation using sufficiently extended Dunning correlation-consistent and Gaussian orbitals, so that interpretations are not basis set dependent. These calculations show that the total exchange repulsion is strongly dependent on the C–C bond lengthening that accompanies rotation. The effect of this relaxation is that the total exchange repulsion favors the eclipsed conformer by ∼6 kcal/mol, far greater than previous estimates obtained without skeletal relaxation. The source of the skeletal flexing dependence stems from the strong dependence of the orthogonalization-induced-energy-shift of the σCH NBO and carbon core orbitals on RC–C. Strong basis set dependence is found for the pairwise repulsions. Extended basis set calculations attribute an antibarrier energy change to anti/syn repulsions and a barrier-forming one to gauche repulsions. These senses are opposite to the barrier-forming anti/syn CH pairwise interactions found in previous ethane steric considerations.

Natural Energy Decomposition Analysis: The Linear Response Electrical Self Energy

An extension of the natural energy decomposition analysis (NEDA) is described that leads to a reduced, three-component treatment of ab initio molecular interaction potentials. These components include the classical electrical (static and induced) and quantum mechanical core (σ−σ) and charge transfer (σ−σ*) interactions. The electrical component is, in turn, represented by three terms: the static interaction of unperturbed fragment charge densities, a contribution involving polarized charge densities, and an electrical self polarization energy. Extended basis set calculations demonstrate the high numerical stability of the three-component NEDA approach. Applications are presented for the Li+(H2O) and water dimer complexes. The long-range behavior of the interaction potentials of these complexes is entirely determined by the classical electrical interaction of the fragments. Core and charge transfer effects are only significant for molecular separations within roughly 1 A of equilibrium.

Electric-field gradient at oxygen sites in RBCO: Effects from a positive muon

A limited quantum chemistry approach has been used to examine changes to the electric-field gradient at oxygen sites in rare-earth barium copper oxides (RBCO) due to a bonded muon (or hydrogen). Results are reported for an all electron, extended basis set calculation for an OMu− molecule which is embedded in various point charge clusters to simulate the RBCO crystal environment. Differences between the gradients for O2− and OMu− are examined for five likely muon bond sites. In each case the muon significantly modifies the calculated gradient.

Extended basis set calculations of the interaction energy and properties of the ammonia dimer

Second-order Møller—Plesset calculations employing large basis sets which include bond functions are presented for (NH3)2. The H-bonded structure is found to be more stable than a cyclic configuration. The nuclear quadrupole coupling constants for the 14N nuclei are shown to be sensitive to rotational motions of the monomers.

Frontier orbital energies in quantitative structure-activity relationships: A comparison of quantum chemical methods

The energies of the highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO) have long been used as descriptors in QSAR (Quantitative Structure-Activity Relationships). It is shown that different quantum chemical methods of calculating these energies yield results which sometimes correlate poorly with each other. This could seriously affect physical interpretation of QSAR equations. A comparison is made between HOMO and LUMO energies and their differences and sums (hardness and electronegativity) calculated by some of the best knownab initio and semi-empirical methods for two series of simple organic molecules. The difference between the HOMO and LUMO energies correlates better between methods than does either alone, and their sum correlates relatively poorly. MINDO/3 (Modified Intermediate Neglect of Differential Overlap, version 3) is the poorest method in terms of correlation with the more extended basis setab initio methods, followed by CNDO (Complete Neglect of Differential Overlap) and INDO (Intermediate Neglect of Differential Overlap). The best semi-empirical methods, in terms of correlation with experiment and the more extended basis setab initio calculations, are MNDO (Modified Neglect of Differential Overlap), AM1 (Austin Model 1) and PM3 (Parametric Method 3). The simplestab initio method, STO-3G, does not agree as well with the extended basis set calculations or with experimental results as the more advanced semi-empirical methods.

Structural Distortion of CH3I in an Ion-Dipole Precursor Complex

Extended basis set calculations including electron correlation are used to calculate the properties of I - .CH 3 I and I - .CD 3 I ion-molecule complexes. The results show smaller geometrical distortions of the molecular entity upon complexation than were inferred from recent experiments

An efficient procedure for calculations of interaction energy in large molecular systems

The recently proposed ab initio method for calculations on molecular systems with the approximation of the inactive part of a molecule by a frozen molecular fragment is applied to the case of ethanol—water interactions. The results from the Hartree—Fock and second-order Møller—Plesset methods are presented. The reproduction of interaction energies and atomic charges is excellent in regard to results from extended basis set calculations. Different choices of fragments to be frozen have been examined.

Splicing I: Using mixed basis sets in ab initio calculations

AbstractThe effect of mixing (or “splicing”) extended and minimal basis sets on molecular properties such as geometries, Mulliken charges, dipoles, and internal rotation barriers was studied for several test molecules. The effect is gauged by comparison with full extended basis set calculations. It is found that splicing improves most properties relative to full minimal basis set calculations, and little accuracy is lost if the splicing is done in a judicious manner.

MRD‐CI calculations of proton affinity within the ab initio method for approximation of the frozen molecular fragment

AbstractThe method of approximation of the frozen molecular fragment (FMF) we derived has been applied to calculations of proton affinities. Results are in good agreement with experimental data and extended basis set calculations.

An ab initio method for approximation of the frozen molecular fragment

AbstractAn ab initio method for calculation on many‐electron molecular systems with the approximation of the inactive part of a molecule by frozen molecular fragment is presented. In the following method the SCF calculations are performed in two series. First the molecular orbitals resulting from the first SCF calculation (modest basis set) are localized. In the second SCF run, the basis set is extended for the active part of the molecule, while molecular orbitals of the inactive part, selected from the localized set, are kept frozen. The results are in good agreement with the extended basis set calculation.

Extended basis set calculations of atomization energies: Comparison of isogyric and direct results

We describe the results of a series of extended basis set Møller-Plesset perturbation theory calculations on a series of first-row hydrides and several multiply bonded compounds. Analysis of atomization energy predictions obtained employing the isogyric reaction technique demonstrates that third-order perturbation theory results are virtually indistinguishable from the results using a full fourth-order calculation, in the case of the hydrides.

The C4H7+ cation. A theoretical investigation.

The potential energy surface of the C4H7+ cation has been investigated with ab initio quantum chemical theory. Extended basis set calculations, including electronic correlation, show that cyclobutyl and cyclopropylcarbinyl cation are equally stable isomers. The saddle point connecting these isomers lies 0.6 kcal/mol above the minima. The global C4H7+ minimum corresponds to the 1-methylallyl cation, which is 9.0 kcal/mol more stable than the cyclobutyl and the cyclopropylcarbinyl cation and 9.5 kcal/mol below the 2-methylallyl cation. These results are in excellent agreement with experimental data.

The C-Li bond in methyllithium. Binding energy and ionic character

Abstract Extended basis set calculations yield a dissociation energy † E (MeLi → Me + Li) = 46.4 ± 1.2 kcal mol −1 . The Me-Li bond has non-negligible covalent contributions. Comparison with the series of Molecules NaF, NaCl, LiF and LiCl shows that the covalent contribution in MeLi is more pronounced than in LiCl.