The computation of some molecular weights

A method is described for deducing the molecular weight of a compound, the mass spectrom of which does not extend as far as the molecular weight, It is based upon the combination of fragment ions and restricted to limits determined by an approximate estimate of that weight.     

The computation of the chemical potential of a fluid

“Non-destructive” computer simulation techniques for evaluating the chemical potential of a fluid are discussed. A simple case is used to obtain explicit analytical expressions for the functions involved. This illustrates the physical content of the statistical-mechanical analysis and is useful in explaining puzzling behaviour and in evaluating data on more realistic models of fluids obtained in this way.     

On the computation of molecular electronic affinities

Using a multireferent MBPT method (CIPSI) the electronic affinity (EA) of F, CN and HCC is computed. Results show how UMP2 gives unbalanced truncation of the MP series, while ROMP2 has the correct (balanced) behaviour. The good agreement with the experimental EA found for some compounds is accidental and associated to an error compensation. The good agreement with the experimental data found for the ROMP2 and CIPSI EAs is analysed.This paper was presented at the International Conference on The Impact of Supercomputers on Chemistry, held at the University of London, London, UK, 13–16 April 1987     

Calculating the electric potential of macromolecules: A simple method for molecular surface triangulation

An improved version of the “marching-cube” method¹ is proposed for molecular surface triangulation. This new algorithm involves fewer and simpler basic building blocks and avoids the artificial gaps of the original one. Moreover, to make it applicable to the boundary element method, the procedures for the protein cavity identification and triangle reduction are also presented. The triangulation procedure was tested by incorporating it into the boundary element method (BEM) to estimate the pK_a values of subtilisin BPN′ and bovine trypsin inhibitor (BPTI). © 1995 by John Wiley & Sons, Inc.     

胰岛素单体、双体分子静电势的计算

计算了三方二锌胰岛素晶胞不对称单位中两个胰岛素分子单体及其双体的分子静电势。结果表明:胰岛素两个单体分子的构象不同,其分子表面静电势也不相同,由于它们的构象是类似的,所以其电势分布也是接近的,单体胰岛素分子的表面静电势呈偶极型分布,双体的表面静电势基本保持单体的特征。文中还比较了两个单体分子及其集聚后的静电势变化。     

The molecular electrostatic potential of the B-DNA helix

The overlap multipole expansion procedure is utilized for the evaluation of the component of the electrostatic molecular potential of the B-DNA helix due to its sugar-phosphate backbone. The overall shape of the potential, its extension in space, the location of the minima and the differences in the values of the potential in particularly significant regions (minor and major grooves, vicinity of the phosphates) are indicated. The isopotential surfaces are practically cylindrical at distances larger than 15 Å from the helix axis but exhibit a more complex structure at shorter distances.This paper is dedicated to Professor H. Hartmann on the occasion of his 65th birthday.     

The molecular electrostatic potential of the B-DNA helix

The influence of a single and double helical DNA environment on the molecular electrostatic potentials at the C₈ and amino sites of guanine and adenine are studied. The results are employed in a tentative explanation of the variation in binding sites of N-acetoxy-N-2-acetylaminofluorene with DNA, following whether the nucleic acid is in a native or denatured state.     

Computing the electric potential of biomolecules: Application of a new method of molecular surface triangulation

A new method is presented for defining a smooth, triangulated analytic surface for biological molecules. The surface produced by the algorithm is well-suited for use with a recently developed polarizationcharge technique¹ for the computation of the electrostatic potential of solvated molecules, and may also be used for calculations of molecular surface areas and volumes. The new method employs Connolly's definitions of contact, reentrant and saddle surface,² but includes modifications that preclude the presence of self-interesting reentrant surface, and also insure a rigorous decomposition of contact regions into curvilinear finite elements. The triangulation algorithm may be used in conjunction with the electrostatic methods described previously to compute the electric potential of molecules of arbitrary shape in solution. Applications include the estimation of hydration enthalpies, computation of the electrostatic forces associated with solvation, estimation of interactions between separate charged species in solution, and computation of the three-dimensional form of the molecular electric potential. Test calculations are presented for a double-stranded dinucleotide, the polypeptide enkephalin, and the protein ferredoxin.     

The rigorous (nonvariational) solution of the Schrödinger equation for a molecular potential of arbitrary shape. II. The basis functions,discrete spectrum,and the special case of MT potential

This paper continues Part I of this paper, referred to in the following as I. The construction of a basis set is explicitly presented. The special case of MT potential is considered, and the corresponding secular equation is shown to match exactly the one resulting from the well-known scattered wave method. Finally, the bound states of a molecule are obtained as the solutions of a real-valued matrix eigenvalue problem.     

Efficient computation of potential energy first and second derivatives for molecular dynamics,normal coordinate analysis,and molecular mechanics calculations

By using two- and three-body internal coordinates and their derivatives as intermediates, it is possible to enormously simplify formulas for three- and four-body internal coordinates and their derivatives. Using this approach, simple formulas are presented for stretch (two-body), two types of bend (three-body), and wag and two types of torsion (four-body) internal coordinates and their first and second derivatives. The formulas are eminently suitable for economizing molecular dynamics and molecular mechanics calculations and normal coordinate analysis of complicated potential energy surfaces. Efficient methods for computing derivatives of entire potential energy terms, and in particular cross terms with switching functions, are presented.     

The effective molecular polarizability and local electric field in molecular crystals

A rigorous treatment of the local electric field is used to calculate effective molecular polarizabilities from optical data for naphthalene, anthracene, phenanthrene and bighenyl crystals. The principal axes of polarizability are typically 10° from the molecular axes, in accord with spectroscopic results. Various applications are outlined.     

The effective molecular polarizability and local electric field in molecular crystals

The problem of calculating the effective molecular polarizabilities and the local electric fields in molecular crystals is considered. It is shown that in a crystal with two or more anisotropic molecules per unit cell, these quantities cannot be found from the crystal structure and the dielectric tensor alone.     

AF molecular rings for quantum computation

Molecular magnets have been recently proposed as possible building blocks for a solid-state quantum computer. In order to substantiate and develop such a proposal, one needs to identify those molecules that are best suited for the qubit encoding and manipulation. Here, we focus on a heterometallic molecular ring, namely Cr₇Ni, where the substitution of one Cr³⁺(S = 3/2) with Ni²⁺(S = 1) provides an extra spin to the otherwise compensated molecule. We show that its ground state consists in an S = 1/2 doublet, energetically well separated (Δ₀/k_B ∼ 13 K at zero magnetic field) from the first excited multiplet. This relatively large value of Δ₀, together with the reduced mixing of the subspaces corresponding to different values of the total spin S, enables a safe encoding of the |0〉 and |1〉 states with the ground-state doublet, and allows to coherently rotate the effective S = 1/2 spin, while keeping the population loss to the excited states negligible. A further, intriguing challenge is represented by the implementation of the conditional dynamics (two-qubit gates). We present here preliminary characterization of molecular “Cr₇Ni-dimers”, i.e., derivatives in which two Cr₇Ni rings are linked with each other by means of delocalized aromatic amines. The resulting intercluster couplings are estimated to be ⩽1 K and are expected to be permanent, i.e., not tuneable during gating, as required by the standard approach to quantum computation. We discuss a computational scheme that allows in principle to overcome this limitation. The most relevant decoherence mechanisms for Cr₇Ni and possible ways to reduce their effects are discussed as well.     

The nuclear electric quadrupole moment of antimony from the molecular method

Relativistic Dirac-Coulomb (DC) Hartree-Fock calculations are employed to obtain the analytic electric field gradient (EFG) on the antimony nucleus in the SbN, SbP, SbF, and SbCl molecules. The electronic correlation contribution to the EFGs is included with the DC-CCSD(T) and DC-CCSD-T approaches, also in the four-component framework, using a finite-difference method. The total EFG results, along with the experimental nuclear quadrupole coupling constants from microwave spectroscopy, allow to derive the nuclear quadrupole moments of (121)Sb and (123)Sb, respectively, as -543(11) and -692(14) mb.     

The electrostatic molecular potential of yeast tRNAPhe. III. The molecular potential and the steric acessibility associated with the phosphate groups

The molecular electrostatic potential of yeast tRNA^Phe is calculated at sites bridging the anionic oxygens of each of the 76 phosphate groups of the molecule. A quantitative measure of the steric accessibility of the anionic oxygens of the phosphates toward a spherical cation is presented. Both the resulting potentials and accessibilities are discussed in terms of the molecular and electronic structure of tRNA.