Solvatons. II. Aqueous dissociation of hydrides in the MINDOS approximation

A simple electrostatic model of solvation is presented which allows the interaction with solvent to be included systematically within semiempirical SCF calculations. Solvent effects are incorporated into the Hamiltonian for a solute molecule through a series of imaginary particles, solvatons, which represent the oriented solvent distribution around the solute.The proposed model is based on an algorithm for approximating the enthalpy of solvation of each atomic center from its charge in the molecular system and the experimental hydration enthalpies of its various ions. The calculated atomic solvation energy of one center is then modified to include the interaction with other charged atomic centers in the molecule. The method, developed here for the MINDO/3 approximation, has been applied to the calculation of the aqueous dissociation of a series of hydrides. In general, it leads to fairly accurate solvation enthalpies andpK _a values when applied to systems with fixed molecular geometries. A general discussion of the problems associated with the development of a solvation model within a semiempirical framework is also presented.     

A programmable spin-free method for configuration interaction

In this note a method is presented for quick implementation of configuration interaction (CI) calculations in molecules. A spin-free Hamiltonian for anN electron system in a spin stateS, expressed in terms of the generators for the unitary group algebra, is diagonalized over orbital configurations forming a basis for the irreducible representation [2^1/2N-S 1^2S ] of the permutation group S _N . It has been found that the basic algebraic expressions necessary for the CI calculation involve a limited category of permutations. These have been displayed explicitly. On leave from the Indian Institute of Technology, Bombay, India.     

Ab initio calculations of the ground-state potential energy surface for the C?F bond decomposition in n-fluoropropane within the method for approximation of the frozen molecular fragment

The recently proposed ab initio method for calculation on many-electron molecular systems with the approximation of the inactive part of a molecule by a frozen molecular fragment was tested further in a case of the dissociation reaction of the C? F bond in n-fluoropropane. Results from the Hartree–Fock, multiple reference double-excitation configuration–interaction and second-order Møller–Plesset methods are presented. The reproduction of potential energy surfaces as well as the reproduction of electron density distribution are in excellent agreement with extended basis-set calculations. Different choices of fragments to be frozen have been examined.     

Polarizable Atomistic Calculation of Site Energy Disorder in Amorphous Alq3

A polarizable molecular dynamics simulation and calculation scheme for site energy disorder is presented in amorphous tris(8‐hydroxyquinolinato)aluminum (Alq₃) by means of the charge response kernel (CRK) method. The CRK fit to the electrostatic potential and the tight‐binding approximation are introduced, which enables modeling of the polarizable electrostatic interaction for a large molecule systematically from an ab initio calculation. The site energy disorder for electron and hole transfers is calculated in amorphous Alq₃ and the effect of the polarization on the site energy disorder is discussed.     

A study of dynamic quadrupolar and octupolar excitations and calculations on excited d and f states of atom and ions: He-sequence

The quadrupolar and octupolar distortion of the ions in the He-sequence caused by an external electro–magnetic field has been studied by a variation–perturbation method in the Hartree–Fock scheme. For certain frequencies singularities appear in the response of the system to the perturbation. Approximate representations for the excited d and f states have been obtained from a study of these resonances. Such a perturbation calculation has the advantage that representations of the different excited states are obtained independently. The orthogonality to all the lower lying levels of the same symmetry is not required. The only source of inaccuracy implicit in the procedure lies in the improper consideration of the inter-electronic interaction. This is corrected for by an independent calculation, which is again formulated in terms of a perturbation treatment. The resulting wave functions for the excited states are accurate in the Hartree–Fock model. Expectation values of several operators have been calculated with these corrected wave functions.     

Quantum-chemical investigation on hydrogen bonding interaction of hydrogen fluoride dimer at various mutual orientations

Hydrogen bonding interaction in hydrogen fluoride dimer has been investigated by quantum-chemical calculation with 6-311G^** basis set at various mutual orientations. Atomic charges and charge transfer have been calculated by means of potential-derived method, and decomposition of hydrogen bonding interaction has been executed. The calculation results show that there is a variation range for the energy-stable orientations, the charge transfer in the range presents maximum value, and the charge transfer interaction plays a decisive role in the hydrogen bonding.     

Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules

The evaluation of water binding free energies around solute molecules is important for the thermodynamic characterization of hydration or association processes. Here, a rapid approximate method to estimate water binding free energies around (bio)macromolecules from a single molecular dynamics simulation is presented. The basic idea is that endpoint free‐energy calculation methods are applied and the endpoint quantities are monitored on a three‐dimensional grid around the solute. Thus, a gridded map of water binding free energies around the solute is obtained, that is, from a single short simulation, a map of favorable and unfavorable water binding sites can be constructed. Among the employed free‐energy calculation methods, approaches involving endpoint information pertaining to actual thermodynamic integration calculations or endpoint information as exploited in the linear interaction energy method were examined. The accuracy of the approximate approaches was evaluated on the hydration of a cage‐like molecule representing either a nonpolar, polar, or charged water binding site and on α‐ and β‐cyclodextrin molecules. Among the tested approaches, the linear interaction energy method is considered the most viable approach. Applying the linear interaction energy method on the grid around the solute, a semi‐quantitative thermodynamic characterization of hydration around the whole solute is obtained. Disadvantages are the approximate nature of the method and a limited flexibility of the solute. © 2016 Wiley Periodicals, Inc.     

A time-dependent molecular orbital approach to electron transfer in ion–metal surface collisions

A time-dependent molecular orbital method has been developed to study charge transfer in collisions of ions with metal surfaces at energies between 1 and 100 au. A set of localized basis functions consisting of generalized Wannier functions for the surface and s- and p-atomic functions for the ion, is used to separate the system into primary and secondary regions. An effective Hamiltonian and time-dependent equations for the electron density matrix are obtained in the primary region, where most charge transfer occurs. The equations for the electron density matrix are solved with a linearization scheme. The method is suitable to study atomic orbital orientation for collisions of ions and surfaces. A model calculation for Na⁺ + W(110) collisions with a prescribed trajectory is presented. The interaction potentials between the W(110) surface and Na⁺ 3s and 3p orbitals are calculated from Na⁺ pseudopotentials. Results show that the yield of neutralized atoms in 3p states changes as the collision energy is lowered.     

Energy deposition mechanisms and biochemical aspects of DNA strand breaks by ionizing radiation

A theoretical model based on physical, chemical, and biochemical mechanisms has been presented to evaluate the yields of DNA strand breaks (single and double) as a function of linear energy transfer (LET ) or ?dE/dx. Energetic heavy charged particles are considered explicitly to provide a general theory for low- as well as for high-LET radiation. There are three main features of the calculation: (a) track structure considerations for the energy deposition pattern, (b) three-dimensional structure of DNA molecules to provide information on the exact location of damage, and (c) a Monte-Carlo scheme to simulate the diffusion processes of water radicals. To avoid the complexities of a cellular medium, an aqueous solution of DNA is considered in the calculation. When the results of the calculations are compared with experimental measurements of the yields of strand breaks in mammalian DNA (exposed in a cellular complex), reasonable agreement is obtained. However, only those experimental data have been compared where there were no enzyme repair processes. The method of calculation has also been extended to study breaks in higher-order structures of DNA molecules such as chromatin. Specific limitations of the present model have been pointed out for making further improvements.     

Novel method of self‐interaction corrections in density functional calculations

It is demonstrated that the commonly applied self‐interaction correction (SIC) used in density functional theory does not remove all self‐interaction. We present as an alternative a novel method that, by construction, is totally free from self‐interaction. The method has the correct asymptotic 1/r dependence. We apply the new theory to localized f electrons in praseodymium and compare with the old version of SIC, the local density approximation (LDA) and with an atomic Hartree–Fock calculation. The results show a lowering of the f level, a contraction of the f electron cloud and a lowering of the total energy by 13 eV per 4 f electron compared to LDA. The equilibrium volume of the new SIC method is close to the ones given by LDA and the older SIC method and is in good agreement with experiment. The experimental cohesive energy is in better agreement using the new SIC method, both compared to LDA and another SIC method. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 247–252, 2001     

Monte Carlo–MST: New strategy for representation of solvent configurational space in solution

A new procedure for the representation of the configurational space of solutes in solution is presented. The method is based on the combination of standard Monte Carlo techniques with the continuum model developed by the Pisa group in its semiclassical version, which was developed by our group. The suitability of the method for exploring the configurational space of chemical systems in solution has been tested by analyzing the dimers of formic acid, imidazole, and benzene, as well as the interaction between the ammonium cation and the formate anion. The results in aqueous solution are compared with those obtained in a gas phase environment. The calculations provide detailed information on the interaction modes between monomers and their contribution to the dimer. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 665–678, 1999     

Interaction of Na, Mg, Al, Si with carbon nanotube (CNT): NMR and IR study

A Quantum Mechanics (QM) is used for investigated the nature of metals transport and interaction with single-walled carbon nanotubes (SWCNTs) inter membranes. Metal species can be transported actively by a combination of SWCNT-membranes conducting channels that have been used for bio-molecular and detection. This study is based on the interaction of Na, Mg, Al, and Si with the structural features of SWCNTs in the ground state ab initio, HF theory and DFT calculation have been performed with the program Gaussian A7 package suite of programs. We used HF and DFT (B3LYP) method for calculation energy, chemical shift nucleus magnetic resonance and proportion thermodynamic by DFT-IR and DFT-NMR for RWCNT in absence and presence metals. The basis set used 6-31G and 6-31G* that increasing electronegativity metals increased the total energy. The proportion SWCNTs were changed by them. In this study presented a comprehensive on effects of metals on SWCNTs, which are on theirs electronic structure, and transfer of charge from metal to SWCNTs. The results are presented for T = 310 K, the temperature of human’s body.     

Numerical studies for a theoretical analysis of semiempirical LCAO–CI methods

A numerical investigation of Del Re and Parr's formulas [1] for the treatment of π systems has been preformed in the case of five-membered rings, using two different expressions for the core Hamiltonian and different values for the effective charges. The results obtained are discussed by analysing the three stages of the calculation: (a) a non-iterative LCAO –MO calculation; (b) the same calculation with corrections for exchange and repulsion terms arising from fluctuations of the orbital populations; (c) configuration interaction. The calculations are interesting also because they do not involve the zero differential overlap approximation; a calculation without inclusion of overlap hse been carried out for pyrrole and the results have been compared with those including S . The main conclusions hold also for σ electrons, and can serve to assess better the validity of simple σ calculations.     

Molecular dynamic study of the anomalous behavior of heat capacity in a methanol-water mixture

The molecular dynamic (MD) method is used to study the anomalous behavior of heat capacity in the range of small concentrations of methanol-water solutions. The behavior of the concentration dependence of heat capacity as calculated by the MD method qualitatively coincides with the experimental values. The calculation of contributions from different types of interaction to heat capacity showed that the greatest contribution is made by the interaction between the methanol molecules. The reason for the anomalous behavior of heat capacity is discussed based on the calculation of the mean force potential, radial distribution functions, and hydrogen bond network parameters. Translated fromZhurnal Strukturnoi Khimii, Vol.40, No. 2, pp. 304–313, March–April, 1999.     

Construction of ternary phase diagrams in nonsolvent/solvent/PMMA systems

In this work, the ternary phase diagrams in three nonsolvent/solvent/PMMA systems (n-hexane/n-butyl acetate/PMMA, water/acetone/PMMA, and n-hexane/acetone/PMMA) were constructed by theoretical calculation and experimental measurement. Binodal curves were calculated by using the Flory–Huggins theory for three-component systems and measured by titrating the PMMA solution with nonsolvent until the onset of turbidity. By using concentration-dependent nonsolvent/solvent and solvent/PMMA interaction parameters and constant nonsolvent/PMMA interaction parameters, good agreement has been obtained between the calculation and the measurement. The values of nonsolvent/solvent interaction parameters were taken from the literature sources, and the values of solvent/PMMA and nonsolvent/PMMA interaction parameters were measured by vapor sorption and swelling equilibrium, respectively. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 607–615, 1998     

Molecular modeling of polymers: I. Correct and efficient enumeration of intrachain conformational energetics

Polymer conformational analyses can require being able to model the intramolecular energetics of a very long (infinite) chain employing calculations carried out on a relatively short chain sequence. A method to meet this need, based upon symmetry considerations and molecular mechanics energetics, has been developed. Given N equivalent degrees of freedom in a linear polymer chain, N unique molecular groups are determined within the chain. A molecular unit is defined as a group of atoms containing backbone rotational degrees of conformational freedom on each of its ends. The interaction of these N molecular groups, each with a finite number of nearest neighbors, properly describe the intramolecular energetics of a long (infinite) polymer chain. Thus, conformational energetics arising from arbitrarily distant neighbor interactions can be included in the estimation of statistical and thermodynamic properties of a linear polymeric system. This approach is called the polymer reduced interaction matrix method (PRIMM) and the results of applying it to isotactic polystyrene (I-PS) are presented by way of example.     

Calculation of the elementary rate constants of polymer-analogous reactions and sequence analysis of products

A method has been developed for the calculation of elementary rate constants of deceleration and acceleration reactions on polymers in which the reactivity of the group is influenced only by the character of the closest adjacent groups. It is suggested that this method may be valid if the calculation yields a rate constant k′₃, which is independent of conversion. In this case, the sequence analysis of products can be performed by using Markovian first-order statistics, and the rate constants thus obtained can be used for calculating the relative frequencies of variously long sequences of reacted and unreacted groups and their number-average length. For markedly accelerated reactions, a simplified method of estimation of the average sequence length involving use of two of the three elementary rate constants, i.e., k₁ and k′₂, has been suggested.     

The fragments-in-molecules method. II. Fim method for σ-bonded systems

A semiempirical SCF MO method has been developed in which the wave function of a composite molecule is written as a linear combination of localized fragment orbitals and which is formulated such that strictly transferable empirical data for the fragments may be introduced into the calculation. Results of FIM calculations in the CNDO /2 approximation for a number of R? X molecules with R = alkyl and X = F, OH, NH₂, and CH₃ are presented and used to illustrate the possibilities and limitations of the method.     

Generalized open shell SCF theory

A generalized form of the coupling operator technique in SCF theory has been developed. In the formalism presented here, the monoconfigurational problem may be treated as a particular case of the multiconfigurational framework. The matrix form of the operators has been analyzed; in the LCAO context a structure has been found which is very adequate for computational purposes. Some examples are also presented which show the usefulness of the theory, emphasising the CNDO and INDO approximations. Within the application of the method to ab initio calculations, some He and second row atoms states have been studied. The He first excited singlet is also studied, the result of the analysis of such a problem being that the nonorthogonality between the singlet functions of the fundamental and of the first excited states play a primordial role in the efficiency of the method. In no case have the calculation problems, appearing in the application of the theory, been of a more difficult nature than those normally found in the application of the formalism for closed shells.     

Anab initio potential energy surface and dynamics calculations for vibrational excitation of I2 by He

We present newab initio calculations of the interaction potential and the elastic and inelastic cross sections for He scattering by I₂. The electronic structure calculations of the interaction potential are based on an extensive one-electron basis set (triple zeta plus ad set on each I, ans function plus ap set at the I₂ bond center, and quadruple zeta plus twop sets on He), a two-configuration-SCF orbital set, and a configuration interaction calculation based on all single and double excitations out of the two-configuration reference space. The calculations are performed at 16He-I₂ distances for nine combinations of I₂ vibrational displacement and orientation. A new form of analytic representation is presented that is particularly well suited to efficient and accurate fitting ofab initio interaction potentials that include vibrational displacements. Scattering calculations are performed by the vibrational close-coupling, rotational-infinite-order-sudden approximation with a converged vibrational basis.