原子结构参数的改进Xa法计算

六十年代后期,在Hartree－Fock-Slater法的基础上,提出了Xα法［1］．用于原子结构计算的Xα法与HF（Hartree－Fock）法的主要区别在于：用简单的统计平均交换势替代了HF法中计算最为困难的电子交换势,从而在保持较高理论严谨性和计算精确度的同时,大大减少了计算工作量,近年来获得了广泛的应用．我们尝试用经过适当修改的Xα方法,计算原子参数,解决分子结构中的某些问题．用原子参数解决分子问题,历来是化学和物理工作者常用的方法．本工作的意图是引入一个比HF法简单的容易在微机上实现的某种表现原子参数的计算方法,提供…     

混合式格点法研究氧在银或银合金表面的吸附动力学

本文改进了混合式格点法对第一时间步的计算方法, 在保持原有精度的基础上, 减少计算时间约三个数量级。用这一方法, 研究了氧在银及其合金表面的吸附动力学。计算表明: 氧分子在银表面有效吸附的反应阈值是6.29kJ/mol, 这和实验所得的活化能相同。当氧分子动量大于45a.u.或合金中金配比大于0.30时,氧分子均无法在银及其合金表面形成稳定吸附, 这此结果和实验一致。计算中没有发现分子氧直接解离成原子氧的现象。从计算结果中推测, 处在振动激发态的氧分子比处在振动基态的氧分子更容易吸附在银表面。     

Construction of a multivariate calibration by the simple interval calculation method

Simple interval calculation is a method for linear modeling and for constructing interval estimates of predictions in a multivariate calibration. Simple interval calculation gives results in a convenient interval form with regard to all the existing uncertainties: measurement errors of predictors and responses, discrepancies of bilinear modeling, and so on. In addition, the simple interval calculation method opens new opportunities for constructing an informative classification of object significance. The method is based on only the assumption of the error boundedness; it uses linear programming algorithms for data analysis. This approach differs substantially from the conventional regression methods used in chemometrics and, therefore, is poorly understood by analysts. This paper gives an elementary explanation of the simple interval calculation method illustrated by the simplest model and real examples.     

Electron tunneling in proteins program

We developed a unique integrated software package (called Electron Tunneling in Proteins Program or ETP) which provides an environment with different capabilities such as tunneling current calculation, semi‐empirical quantum mechanical calculation, and molecular modeling simulation for calculation and analysis of electron transfer reactions in proteins. ETP program is developed as a cross‐platform client‐server program in which all the different calculations are conducted at the server side while only the client terminal displays the resulting calculation outputs in the different supported representations. ETP program is integrated with a set of well‐known computational software packages including Gaussian, BALLVIEW, Dowser, pKip, and APBS. In addition, ETP program supports various visualization methods for the tunneling calculation results that assist in a more comprehensive understanding of the tunneling process. © 2016 Wiley Periodicals, Inc.     

Electrostatic energies and forces computed without explicit interparticle interactions: a linear time complexity formulation

A rapid method for the calculation of the electrostatic energy of a system without a cutoff is described in which the computational time grows linearly with the number of particles or charges. The inverse of the distance is approximated as a polynomial, which is then transformed into a function whose terms involve individual particles, instead of particle pairs, by a partitioning of the double sum. In this way, the electrostatic energy that is determined by the interparticle interactions is obtained without explicit calculation of these interactions. For systems of positive charges positioned on a face-centered cubic lattice, the calculation of the energy by the new method is shown to be faster than the calculation of the exact energy, in many cases by an order of magnitude, and to be accurate to within 1-2%. The application of this method to increase the accuracy of conventional truncation-based calculations in condensed-phase systems is also demonstrated by combining the approximated long-range electrostatic interactions with the exact short-range interactions in a "hybrid" calculation. For a 20-A sphere of water molecules, the forces are shown to be six times as accurate using this hybrid method as those calculated with conventional truncation of the electrostatic energy function at 12 A. This is accomplished with a slight increase in speed, and with a sevenfold increase in speed relative to the exact all-pair calculation. Structures minimized with the hybrid function are shown to be closer to structures minimized with an exact all-pair electrostatic energy function than are those minimized with a conventional 13-A cutoff-based electrostatic energy function. Comparison of the energies and forces calculated with the exact method illustrate that the absolute errors obtained with standard truncation can be very large. The extension of the current method to other pairwise functions as well as to multibody functions, is described.     

Starting SCF calculations by superposition of atomic densities

We describe the procedure to start an SCF calculation of the general type from a sum of atomic electron densities, as implemented in GAMESS-UK. Although the procedure is well known for closed-shell calculations and was already suggested when the Direct SCF procedure was proposed, the general procedure is less obvious. For instance, there is no need to converge the corresponding closed-shell Hartree-Fock calculation when dealing with an open-shell species. We describe the various choices and illustrate them with test calculations, showing that the procedure is easier, and on average better, than starting from a converged minimal basis calculation and much better than using a bare nucleus Hamiltonian.     

A new quantum method for electrostatic solvation energy of protein

A new method that incorporates the conductorlike polarizable continuum model (CPCM) with the recently developed molecular fractionation with conjugate caps (MFCC) approach is developed for ab initio calculation of electrostatic solvation energy of protein. The application of the MFCC method makes it practical to apply CPCM to calculate electrostatic solvation energy of protein or other macromolecules in solution. In this MFCC-CPCM method, calculation of protein solvation is divided into calculations of individual solvation energies of fragments (residues) embedded in a common cavity defined with respect to the entire protein. Besides computational efficiency, the current approach also provides additional information about contribution to protein solvation from specific fragments. Numerical studies are carried out to calculate solvation energies for a variety of peptides including alpha helices and beta sheets. Excellent agreement between the MFCC-CPCM result and those from the standard full system CPCM calculation is obtained. Finally, the MFCC-CPCM calculation is applied to several real proteins and the results are compared to classical molecular mechanics Poisson-Boltzmann (MM/PB) and quantum Divid-and-Conque Poisson-Boltzmann (D&C-PB) calculations. Large wave function distortion energy (solute polarization energy) is obtained from the quantum calculation which is missing in the classical calculation. The present study demonstrates that the MFCC-CPCM method is readily applicable to studying solvation of proteins.     

Fast summation boundary element method for calculating solvation free energies of macromolecules

We present a boundary element method (BEM) for calculating the reaction field energy of a macromolecule embedded in a high-dielectric medium such as water. In a BEM calculation, the key computational task is the calculation of the induced surface charge distribution at the dielectric boundary. This is obtained by solving a system of linear equations whose dimension can run into the tens of thousands for a macromolecule. In this work, we use a fast summation hierarchical multipole method to solve for the induced surface charge densities. By careful analysis of the levels of approximation required for the various terms in the calculation, we avoid the unnecessary computation of terms that contribute negligibly to the final outcome and, consequently, achieve high computational efficiency. For a protein such as BPTI with 890 atoms, the calculation of the induced surface charge density distribution and the reaction field energy was completed in 7.9 s on an SGI workstation with an R10000 CPU. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1494–1504, 1998     

A calculation scheme for estimation of dielectric loss factors in polymers

For the quantitative estimation of dielectric loss tangent tanδ in linear and network polymers, the calculation scheme based on the Debye theory is proposed. The calculation is performed for both polar and nonpolar dielectrics in a wide frequency interval ranging from 10² to 10⁶ Hz. This calculation requires knowledge of only the chemical structure of a repeating unit in a linear polymer or a repeating fragment in a polymer network. Experiments on the estimation of frequency dependences of tanδ are conducted for polymer networks based on poly(urethanes) and poly(isocyanurates) of different compositions. A fair correlation between calculation and experimental data is obtained. It has been shown that tanδ tends to change with the increasing content of bulky isocyanurate network junctions that are responsible for the specific behavior of the system under the action of alternating mechanical and electric fields.     

Calculation of the circular dichroism spectra of carbon monoxy- and deoxy myoglobin: interpretation of a time-resolved circular dichroism experiment

A calculation of the circular dichroism (CD) spectra of carbon monoxy- and deoxy myoglobin is carried out in relation with a time-resolved CD experiment. The calculation is based on the polarizability theory and the parameters are adjusted to fit the experimental absorption and CD spectra. By performing the calculation for intermediate configurations of the protein, we are able to propose an explanation of the CD structure observed on a sub-100 ps time scale. The role of the proximal histidine is, in particular, clearly demonstrated in the first step of the myoglobin relaxation from its liganded to it deliganded form.     

Ab initio electron propagator theory of molecular wires. I. Formalism

Ab initio electron propagator methodology may be applied to the calculation of electrical current through a molecular wire. A new theoretical approach is developed for the calculation of the retarded and advanced Green functions in terms of the electron propagator matrix for the bridge molecule. The calculation of the current requires integration in a complex half plane for a trace that involves terminal and Green's-function matrices. Because the Green's-function matrices have complex poles represented by matrices, a special scheme is developed to express these "matrix poles" in terms of ordinary poles. An expression for the current is derived for a terminal matrix of arbitrary rank. For a single terminal orbital, the analytical expression for the current is given in terms of pole strengths, poles, and terminal matrix elements of the electron propagator. It is shown that Dyson orbitals with high pole strengths and overlaps with terminal orbitals are most responsible for the conduction of electrical current.     

Analytic calculation of isotropic hyperfine structure constants using the normalized elimination of the small component formalism

Based on the normalized elimination of the small component relativistic formalism, a new approach to the calculation of hyperfine structure parameters of paramagnetic molecules is developed and implemented. The new method is tested in the calculation of the isotropic hyperfine structure constant for a series of open-shell molecules containing mercury. The results of calculations carried out in connection with ab initio methods of increasing complexity demonstrate the high accuracy of the formalism developed. In view of its computational simplicity, the new approach provides the basis for an efficient and accurate calculation of the HFS parameters of large molecules.     

THE CALCULATION OF CHEMICAL SHIFTS IN DISUBSTITUTED NAPHTHALENES

<正> The principle and method for calculating the chemical shifts of substituted benzenes have been extended to the calculation of chemical shifts in disubstituted naphthalenes. We have set up a series of empirical parameters for the calculation of chemical shifts. The calculated results of 439 8 values from 78 compounds show that the standard deviation between the calculated and the experimental values is 0.08 ppm. The combination of this calculation with that of the coupling constants can be used to provide a criterion .for the determination of molecular structure in disubstituted naphthalenes as well as to assign NMR parameters for the experiment of proton simulated spectra of disubstituted naphthalenes.     

To what extent can an uncertainty calculation be general?

 It is argued that results of uncertainty calculations in chemical analysis should be taken into consideration with some caution owing to their limited generality. The issue of the uncertainty in uncertainty estimation is discussed in two aspects. The first is due to the differences between procedure-oriented and result-oriented uncertainty assessments, and the second is due to the differences between the theoretical calculation of uncertainty and its quantication using the validation (experimental) data. It is shown that the uncertainty calculation for instrumental analytical methods using a regression calibration curve is result-oriented and meaningful only until the next calibration. A scheme for evaluation of the uncertainty in uncertainty calculation by statistical analysis of experimental data is given and illustrated with examples from the author's practice. Some recommendations for the design of corresponding experiments are formulated.     

Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses,a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses

We propose a free energy calculation method for receptor–ligand binding, which have multiple binding poses that avoids exhaustive enumeration of the poses. For systems with multiple binding poses, the standard procedure is to enumerate orientations of the binding poses, restrain the ligand to each orientation, and then, calculate the binding free energies for each binding pose. In this study, we modify a part of the thermodynamic cycle in order to sample a broader conformational space of the ligand in the binding site. This modification leads to more accurate free energy calculation without performing separate free energy simulations for each binding pose. We applied our modification to simple model host–guest systems as a test, which have only two binding poses, by using a single decoupling method (SDM) in implicit solvent. The results showed that the binding free energies obtained from our method without knowing the two binding poses were in good agreement with the benchmark results obtained by explicit enumeration of the binding poses. Our method is applicable to other alchemical binding free energy calculation methods such as the double decoupling method (DDM) in explicit solvent. We performed a calculation for a protein–ligand system with explicit solvent using our modified thermodynamic path. The results of the free energy simulation along our modified path were in good agreement with the results of conventional DDM, which requires a separate binding free energy calculation for each of the binding poses of the example of phenol binding to T4 lysozyme in explicit solvent. © 2019 Wiley Periodicals, Inc.     

Calculation of molecular electronic spectra by projected-unrestricted Hartree–Fock theory

This paper is concerned with a new application of projected-unrestricted Hartree–Fock theory, namely, the calculation of electronic spectra for symmetric molecules. The excited electronic state is represented by a single determinant whose unrestricted nature allows for orbital rearrangement relative to the self-consistent ground state. The self-consistent calculation must be followed by spin projection to obtain appropriate spin eigenstates. It was necessary to develop modified procedures for portions of the spin projection calculation because our method of constructing the wave functions produces degeneracies among the natural orbitals. Illustrative calculations using the all-valence-electron INDO approximations produced results which compared favorably with configuration-interaction treatments. The method described here should be most useful, however, in conjunction with ab initio calculations using flexible basis sets.     

New method for parallel computation of Hessian matrix of conformational energy function in internal coordinates

A new algorithm for parallel calculation of the second derivatives (Hessian) of the conformational energy function of biomolecules in internal coordinates is proposed. The basic scheme of this algorithm is the division of the entire calculation of the Hessian matrix (called "task") into subtasks and the optimization of the assignment of processors to each subtask by considering both the load balancing and reduction of the communication cost. A genetic algorithm is used for this optimization considering the dependencies between subtasks. We applied this method to a glutaminyl transfer RNA (Gln-tRNA) molecule for which the scalability of our previously developed parallel algorithm was significantly decreased when the large number of processors was used. The speedup for the calculation was 32.6 times with 60 processors, which is considerably better than the speedup for our previously reported parallel algorithm. The elapsed time for the calculation of subtasks, data sending, and data receiving was analyzed, and the effect of the optimization using the genetic algorithm is discussed.     

All-electron density functional calculation on insulin with quasi-canonical localized orbitals

An all-electron density functional (DF) calculation on insulin was performed by the Gaussian-based DF program, ProteinDF. Quasi-canonical localized orbitals (QCLOs) were used to improve the initial guess for the self-consistent field (SCF) calculation. All calculations were carried out by parallel computing on eight processors of an Itanium2 cluster (SGI Altix3700) with a theoretical peak performance of 41.6 GFlops. It took 35 h for the whole calculation. Insulin is a protein hormone consisting of two peptide chains linked by three disulfide bonds. The numbers of residues, atoms, electrons, orbitals, and auxiliary functions are 51, 790, 3078, 4439, and 8060, respectively. An all-electron DF calculation on insulin was successfully carried out, starting from connected QCLOs. Regardless of a large molecule with complicated topology, the differences in the total energy and the Mulliken atomic charge between initial and converged wavefunctions were very small. The calculation proceeded smoothly without any trial and error, suggesting that this is a promising method to obtain SCF convergence on large molecules such as proteins.     

Vibrational coupled cluster theory

The theory and first implementation of a vibrational coupled cluster (VCC) method for calculations of the vibrational structure of molecules is presented. Different methods for introducing approximate VCC methods are discussed including truncation according to a maximum number of simultaneous mode excitations as well as an interaction space order concept is introduced. The theory is tested on calculation of anharmonic frequencies for a three-mode model system and a formaldehyde quartic force field. The VCC method is compared to vibrational self-consistent-field, vibrational M?ller-Plesset perturbation theory, and vibrational configuration interaction (VCI). A VCC calculation typically gives higher accuracy than a corresponding VCI calculation with the same number of parameters and the same formal operation count.     

Periodic calculations of excited state properties for solids using a semiempirical approach

The semiempirical SCF MO method MSINDO (modified symmetrically orthogonalized intermediate neglect of differential overlap) [T. Bredow and K. Jug, Electronic Encyclopedia of Computational Chemistry, 2004] is extended to the calculation of excited state properties through implementation of the configuration interaction singles (CIS) approach. MSINDO allows the calculation of periodic systems via the cyclic cluster model (CCM) [T. Bredow et al., J. Comput. Chem., 2001, 22, 89] which is a direct-space approach and therefore can be in principle combined with all molecular quantum-chemical techniques. The CIS equations are solved for a cluster with periodic boundary conditions using the Davidson-Liu iterative block diagonalization approach. As a proof-of-principle, MSINDO-CCM-CIS is applied for the calculation of optical spectra of ZnO and TiO(2), oxygen-defective rutile, and F-centers in NaCl. The calculated spectra are compared to available experimental and theoretical literature data. After re-adjustment of the empirical parameters the quantitative agreement with experiment is satisfactory. The present approximate approach is one of the first examples of a quantum-chemical methodology for solids where excited states are correctly described as n-electron state functions. After careful benchmark testing it will allow calculation of photophysical and photochemical processes relevant to materials science and catalysis.