Modeling of Magic Water Clusters(H20)2 and (H20)21H+ with the PM3 Quantum-Mechanical Method

The PM3 quantum-mechanical method is able to model the magic water clusters (H20),, and (H20)&+. Results indicate that the H30+ ion is tightly bound within the (H20),, cluster by multiple hydrogen bonds, causing deformation to the symmetric (HzO),, pentagonal dodecahedron structure. The structures, energetics, and hydrogen bond patterns of six local minima (H20)21H+ clusters are presented.

Ability of the PM3 Quantum Mechanical Method to Model Intermolecular Hydrogen Bonding between Neutral Molecules

The PM3 semiempirical quantum-mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02-0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an absolute magnitude greater than 2 kcal mol-' suggest that the global minimum is a hydrogen bonded complex; absolute energies less than 2 kcal mol-' imply that other van der Waals complexes are more stable. The geometries of the PM3 hydrogen bonded complexes agree with high-resolution spectroscopic observations, gas electron diffraction data, and high-level ab initio calculations. The main limitations in the PM3 method are the underestimation of hydrogen bond lengths by 0.1-0.2 for some systems and the underestimation of reliable experimental hydrogen bond energies by approximately 1-2 kcal mol-l. The PM3 method predicts that ammonia is a good hydrogen bond acceptor and a poor hydrogen donor when interacting with neutral molecules. Electronegativity differences between F, N, and 0 predict that donor strength follows the order F > 0 > N and acceptor strength follows the order N > 0 > F. In the calculations presented in this article, the PM3 method mirrors these electronegativity differences, predicting the F-H- - -N bond to be the strongest and the N-H- - -F bond the weakest. It appears that the PM3 Hamiltonian is able to model hydrogen bonding because of the reduction of two-center repulsive forces brought about by the parameterization of the Gaussian core-core interactions. The ability of the PM3 method to model intermolecular hydrogen bonding means reasonably accurate quantum-mechanical calculations can be applied to small biologic systems.

Quantum-Mechanical Investigation of Large Water Clusters

The PM3 quantum-mechanical method has been used to study large water clusters ranging from 8 to 42 water molecules. These large clusters are built from smaller building blocks. The building blocks include cyclic tetramers, pentamers, octamers, and a pentagonal dodecahedron cage. The correlations between the strain energy resulting from bending of the hydrogen bonds formed by different cluster motifs and the number of waters involved in the cluster are discussed. The PM3 results are compared with TIP4P potential and ab initio results. The number of net hydrogen bonds per water increases with the cluster size. This places a limit on the size of clusters that would fit the Benson model of liquid water. Many of the 20-mer clusters fit the Benson model well. Calculations of the ion cluster (H20)4o(H30+)2 reveal that the m/e ratio obtainable by mass spectrometry experiments can uniquely indicate the conformation of the 20 water pentagonal dodecahedron cage present in the larger clusters.

Dynamic polarizability, Cauchy moments, and the optical absorption spectrum of liquid water: A sequential molecular dynamics/quantum mechanical approach

The dynamic polarizability and optical absorption spectrum of liquid water in the 6-15 eV energy range are investigated by a sequential molecular dynamics (MD)/quantum mechanical approach. The MD simulations are based on a polarizable model for liquid water. Calculation of electronic properties relies on time-dependent density functional and equation-of-motion coupled-cluster theories. Results for the dynamic polarizability, Cauchy moments, S(-2), S(-4), S(-6), and dielectric properties of liquid water are reported. The theoretical predictions for the optical absorption spectrum of liquid water are in good agreement with experimental information.

Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study

The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares 〈 V2 〉 and the energies of basepair triplets X G+ Y and X A+ Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B -DNA structure and show that in several important cases the couplings calculated for the idealized B -DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ∼0.07 eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The X G+ Y are by 0.5 eV more stable than X A+ Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA

Toward on-the-fly quantum mechanical/molecular mechanical (QM/MM) docking: development and benchmark of a scoring function.

We address the challenges of treating polarization and covalent interactions in docking by developing a hybrid quantum mechanical/molecular mechanical (QM/MM) scoring function based on the semiempirical self-consistent charge density functional tight-binding (SCC-DFTB) method and the CHARMM force field. To benchmark this scoring function within the EADock DSS docking algorithm, we created a publicly available dataset of high-quality X-ray structures of zinc metalloproteins ( http://www.molecular-modelling.ch/resources.php ). For zinc-bound ligands (226 complexes), the QM/MM scoring yielded a substantially improved success rate compared to the classical scoring function (77.0% vs 61.5%), while, for allosteric ligands (55 complexes), the success rate remained constant (49.1%). The QM/MM scoring significantly improved the detection of correct zinc-binding geometries and improved the docking success rate by more than 20% for several important drug targets. The performance of both the classical and the QM/MM scoring functions compare favorably to the performance of AutoDock4, AutoDock4Zn, and AutoDock Vina.

Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study

The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares 〈 V2 〉 and the energies of basepair triplets X G+ Y and X A+ Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B -DNA structure and show that in several important cases the couplings calculated for the idealized B -DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ∼0.07 eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The X G+ Y are by 0.5 eV more stable than X A+ Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA

On the quantum mechanical propagator for driven coupled harmonic oscillators

The exact propagator beyond and at caustics for a pair of coupled and driven oscillators with different frequencies and masses is calculated using the path-integral approach. The exact wavefunctions and energies are also presented. Finally the propagator is re-calculated through an alternative method, using the δfunction. © 1992 IOP Publishing Ltd.

Quantum mechanical study of YTiO3 to the investigation of piezoelectricity

In previous articles we reported through theoretical studies the piezoelectric effect in BaTiO3, SmTiO3, and YFeO3. In this paper, we used the Douglas-Kroll-Hess (DKH) second-order scalar relativistic method to investigate the piezoelectricity in YTiO3. In the calculations we used the [6s4p] and [10s5p4d] Gaussian basis sets for the O (3P) and Ti (5S) atoms, respectively, from the literature in combination with the (30s21p16d)/[15s9p6d] basis set for the Y ( 3D) atom, obtained by generator coordinate Hartree-Fock (GCHF) method, and they had their quality evaluated using calculations of total energy and orbital energies (HOMO and HOMO-1) of the 2TiO+1 and 1YO+1 fragments. The dipole moment, the total energy, and the total atomic charges in YTiO3 in C s space group were calculated. When we analyze those properties we verify that it is reasonable to believe that YTiO3 does not present piezoelectric properties. Copyright © 2011 Raimundo Dirceu de Paula Ferreira et al.

Ab initio quantum mechanical investigation of structural and chemical-physical properties of selected minerals for minero-petrological, structural ceramic and biomaterial applications

The purpose of this thesis is the atomic-scale simulation of the crystal-chemical and physical (phonon, energetic) properties of some strategically important minerals for structural ceramics, biomedical and petrological applications. These properties affect the thermodynamic stability and rule the mineral-environment interface phenomena, with important economical, (bio)technological, petrological and environmental implications. The minerals of interest belong to the family of phyllosilicates (talc, pyrophyllite and muscovite) and apatite (OHAp), chosen for their importance in industrial and biomedical applications (structural ceramics) and petrophysics. In this thesis work we have applicated quantum mechanics methods, formulas and knowledge to the resolution of mineralogical problems ("Quantum Mineralogy”). The chosen theoretical approach is the Density Functional Theory (DFT), along with periodic boundary conditions to limit the portion of the mineral in analysis to the crystallographic cell and the hybrid functional B3LYP. The crystalline orbitals were simulated by linear combination of Gaussian functions (GTO). The dispersive forces, which are important for the structural determination of phyllosilicates and not properly con-sidered in pure DFT method, have been included by means of a semi-empirical correction. The phonon and the mechanical properties were also calculated. The equation of state, both in athermal conditions and in a wide temperature range, has been obtained by means of variations in the volume of the cell and quasi-harmonic approximation. Some thermo-chemical properties of the minerals (isochoric and isobaric thermal capacity) were calculated, because of their considerable applicative importance. For the first time three-dimensional charts related to these properties at different pressures and temperatures were provided. The hydroxylapatite has been studied from the standpoint of structural and phonon properties for its biotechnological role. In fact, biological apatite represents the inorganic phase of vertebrate hard tissues. Numerous carbonated (hydroxyl)apatite structures were modelled by QM to cover the broadest spectrum of possible biological structural variations to fulfil bioceramics applications.

Further Quantum Mechanical Evidence that Difluorotoluene does not Hydrogen Bond

Calculations were run on the methylated DNA base pairs adenine:thymine and adenine:difluorotoluene to further investigate the hydrogen-bonding properties of difluorotoluene (F). Geometries were optimized using hybrid density functional theory. Single-point calculations at the MP2(full) level were performed to obtain more rigorous energies. The functional counterpoise method was used to correct for the basis set superposition error (BSSE), and the interaction energies were also corrected for fragment relaxation. These corrections brought the B3LYP and MP2 interaction energies into excellent agreement. In the gas phase, the Gibbs free energies calculated at the B3LYP and MP2 levels of theory predict that A and T will spontaneously form an A:T pair while A:F spontaneously dissociates into A and F. Solvation effects on the pairing of the bases were explored using implicit solvent models for water and chloroform. In aqueous solution, both A:T and A:F are predicted to dissociate into their component monomers. Semiempirical calculations were performed on small sections of B-form DNA containing the two pairs, and the results provide support for the concept that base stacking is more important than hydrogen bonding for the stability of the A:F pair within a DNA helix.

Febrifugine derivative antimalarial activity: quantum mechanical predictors

Plasmodium falciparum resistant strain development has encouraged the search for new antimalarial drugs. Febrifugine is a natural substance with high activity against P. falciparum presenting strong emetic property and liver toxicity, which prevent it from being used as a clinical drug. The search for analogues that could have a better clinical performance is a current topic. We aim to investigate the theoretical electronic structure by means of febrifugine derivative family semi-empirical molecular orbital calculations, seeking the electronic indexes that could help the design of new efficient derivatives. The theoretical results show there is a clustering in well-defined ranges of several electronic indexes of the most selective molecules. The model proposed for achieving high selectivity was tested with success.

Controlling the transport of an ion: classical and quantum mechanical solutions

The accurate transport of an ion over macroscopic distances represents a challenging control problem due to the different length and time scales that enter and the experimental limitations on the controls that need to be accounted for. Here, we investigate the performance of different control techniques for ion transport in state-of-the-art segmented miniaturized ion traps. We employ numerical optimization of classical trajectories and quantum wavepacket propagation as well as analytical solutions derived from invariant based inverse engineering and geometric optimal control. The applicability of each of the control methods depends on the length and time scales of the transport. Our comprehensive set of tools allows us make a number of observations. We find that accurate shuttling can be performed with operation times below the trap oscillation period. The maximum speed is limited by the maximum acceleration that can be exerted on the ion. When using controls obtained from classical dynamics for wavepacket propagation, wavepacket squeezing is the only quantum effect that comes into play for a large range of trapping parameters. We show that this can be corrected by a compensating force derived from invariant based inverse engineering, without a significant increase in the operation time.

On the quantum mechanical scattering statistics of many particles

The probability of a quantum particle being detected in a given solid angle is determined by the S-matrix. The explanation of this fact in time-dependent scattering theory is often linked to the quantum flux, since the quantum flux integrated against a (detector-) surface and over a time interval can be viewed as the probability that the particle crosses this surface within the given time interval. Regarding many particle scattering, however, this argument is no longer valid, as each particle arrives at the detector at its own random time. While various treatments of this problem can be envisaged, here we present a straightforward Bohmian analysis of many particle potential scattering from which the S-matrix probability emerges in the limit of large distances.

Electronic properties of liquid hydrogen fluoride: A sequential quantum mechanical/Born-Oppenheimer molecular dynamics approach

The electronic properties of liquid hydrogen fluoride (HF) were investigated by carrying out sequential quantum mechanics/Born-Oppenheimer molecular dynamics. The structure of the liquid is in good agreement with recent experimental information. Emphasis was placed on the analysis of polarisation effects, dynamic polarisability and electronic excitations in liquid HF. Our results indicate an increase in liquid phase of the dipole moment (similar to 0.5 D) and isotropic polarisability (5%) relative to their gas-phase values. Our best estimate for the first vertical excitation energy in liquid HF indicates a blue-shift of 0.4 +/- 0.2 eV relative to that of the gas-phase monomer (10.4 eV). (C) 2010 Elsevier B.V. All rights reserved.