Bond centred functions in relativistic and non-relativistic calculations for diatomics

In this paper, we discuss the performance of molecular basis sets consisting of atomic centred (AC) functions augmented with bond centred (BC) functions in relativistic and non-relativistic calculations carried out at the Hartree–Fock and several correlated levels of approximation. While usually non-correlated calculations employing BC functions can be performed at a lower computational cost as compared with those making use of energy optimized AC basis sets, the correlated calculations are always more accurate and less expensive with the latter. It is demonstrated that both correlated or non-correlated calculations always benefit from the addition of a few BC functions with a moderate increase of computational effort. The performance of basis sets containing even-tempered BC functions is also studied and their usage is advocated in case of relativistic calculations.     

Quantum mechanical study of regioselectivity of radical additions to substituted olefins

Regiochemical trends in the addition of free radicals to substituted olefins are investigated by different quantum chemical approaches with special reference to oxygen centered radicals. From a methodological point of view, density functional methods provide correct general trends but they do not reach quantitative accuracy, especially for intermediate complexes. More reliable results are obtained by single point post‐Hartree–Fock computations at density functional geometries. A number of test computations show that reoptimization of the geometry and computation of vibrational frequencies by correlated methods can be safely avoided. As a consequence, the overall computational approach has very reasonable computer costs. From a more chemical point of view, a careful analysis of computational results points out the significant role of anomeric and polar effects in tuning the common filicity of carbon centered radicals. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 675–691, 2000     

Parallel molecular computations of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly

Self-assembling DNA nanostructures are an efficient means of executing parallel molecular computations. However, previous experimental demonstrations of computations by DNA tile self-assembly only allowed for one set of distinct input to be processed at a time. Here, we report the multibit, parallel computation of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly. A set of DNA tiles encoding the truth table for the XOR logical operation was constructed. Parallel tile self-assembly and ligation led to the formation of reporter DNA strands which encoded both the input and the output of the computations. These reporter strands provided a molecular look-up table containing all possible pairwise XOR calculations up to a certain input size. The computation was readout by sequencing the cloned reporter strands. This is the first experimental demonstration of a parallel computation by DNA tile self-assembly in which a large number of distinct input were simultaneously processed.     

Efficient correlation-corrected vibrational self-consistent field computation of OH-stretch frequencies using a low-scaling algorithm

The authors present a new computational scheme to perform accurate and fast direct correlation-corrected vibrational self-consistent field (CC-VSCF) computations for a selected number of vibrational modes, which is aimed at predicting a few vibrations in large molecular systems. The method is based on a systematic selection of vibrational mode-mode coupling terms, leading to the direct ab initio construction of a sparse potential energy surface. The computational scaling of the CC-VSCF computation on the generated surface is then further reduced by using a screening procedure for the correlation-correction contributions. The proposed method is applied to the computation of the OH-stretch frequency of five aliphatic alcohols. The authors investigate the influence of different pseudopotential and all-electron basis sets on the quality of the correlated potential energy surfaces computed and on the OH-stretch frequencies calculated for each surface. With the help of these test systems, the authors show that their method offers a computational scaling that is two orders of magnitude lower than a standard CC-VSCF method and that it is of equal accuracy.     

Particle formation and surface processes on atmospheric aerosols: A review of applied quantum chemical calculations

Aerosols significantly influence atmospheric processes such as cloud nucleation, heterogeneous chemistry, and heavy-metal transport in the troposphere. The chemical and physical complexity of atmospheric aerosols results in large uncertainties in their climate and health effects. In this article, we review recent advances in scientific understanding of aerosol processes achieved by the application of quantum chemical calculations. In particular, we emphasize recent work in two areas: new particle formation and heterogeneous processes. Details in quantum chemical methods are provided, elaborating on computational models for prenucleation, secondary organic aerosol formation, and aerosol interface phenomena. Modeling of relative humidity effects, aerosol surfaces, and chemical kinetics of reaction pathways is discussed. Because of their relevance, quantum chemical calculations and field and laboratory experiments are compared. In addition to describing the atmospheric relevance of the computational models, this article also presents future challenges in quantum chemical calculations applied to aerosols.     

Hydrogen Bonding in Fluorinated Amides: FTIR,Two Dimensional Correlation Spectroscopy and DFT Calculations

Fluorinated macromers with amidic functional groups are used as additives in several high tech applications. We show here how aggregation phenomena related to hydrogen bonding are one of the key factor determining their chemical/physical and macroscopic properties. IR spectra are analyzed depending on different external parameters such as the concentration of amide groups and temperature. The experimental findings have been interpreted by means of DFT (Density Functional Theory) calculations on suitable molecular models. Moreover, 2D correlation spectroscopy has been applied to different sets of data, considering concentration and temperature as perturbing variables. The two dimensional correlation approaches confirmed the computational results and give an overall interpretation of the effects due to concentration and temperature.     

Correction to DFT interaction energies by an empirical dispersion term valid for a range of intermolecular distances

The computation of intermolecular interaction energies via commonly used density functionals is hindered by their inaccurate inclusion of medium and long range dispersion interactions. Practical computation of inter- and intra-macrobiomolecule interaction energies, in particular, requires a fairly accurate yet not overly expensive methodology. It is also desirable to compute intermolecular energies not only at their equilibrium (lowest energy) configurations but also over a range of biophysically relevant distances. We present a method to compute intermolecular interaction energies by including an empirical correction for dispersion which is valid over a range of intermolecular distances. This is achieved by optimizing parameters that moderate the empirical correction by explicit comparison of density functional (B3LYP) energies with distance-dependent (DD) reference values obtained at the CCSD(T)/CBS limit. The resulting method, hereafter referred to as B3LYP-DD, yields interaction energies with an accuracy generally better than 1 kcal mol(-1) for different types of noncovalent complexes, over a range of intermolecular distances and interaction strengths, relative to the expensive CCSD(T)/CBS standard. For a training set of dispersion interacting complexes, B3LYP-DD interaction energies in combination with diffuse functions display absolute errors equal to or smaller than 0.68 kcal mol(-1). The empirical correction does not significantly increase the computational cost as compared to standard density functional calculations. Applications relevant to biomolecular energy and structure, such as prediction of DNA base-pair interactions, are also presented.     

Comments on the topic “computation of large molecules”

Quantum chemical and molecular modeling computations on large molecular systems are defined for the computational facilities assumed to be available from now to the next 4 years. We considered a few topics which are requiring much attention. The correlation energy is discussed in some detail and we have presented two new functionals, called the J-functional and the K-functional, which make use of Coulomb or exchange-type integrals. In addition, we report new computational results for the Coulomb-Hole-Hartree-Fock approximation. Very brief summaries on new developments in relativistic Dirac-Fock computation and in density functional theory, on the advantages gained by using different basis sets in the same computation, and on the promises of parallel computing conclude the article. © 1996 John Wiley & Sons, Inc.     

Molybdenum Disulphide Precipitation in Jet Reactors: Introduction of Kinetics Model for Computational Fluid Dynamics Calculations

In our previous work, we used the population balance method to develop a molybdenum disulphide kinetics model consisting of a set of differential equations and constants formulated to express the kinetics of complex chemical reactions leading to molybdenum disulphide precipitation. The purpose of the study is to improved the model to describe the occurring phenomena more thoroughly and have introduced computational fluid dynamics (CFD) modelling to conduct calculations for various reactor geometries. CFD simulations supplemented with our nucleation and growth kinetics model can predict the impact of mixing conditions on particle size with good accuracy. This introduces another engineering tool for designing efficient chemical reactors.     

Development of hardware accelerator for molecular dynamics simulations: a computation board that calculates nonbonded interactions in cooperation with fast multipole method

Evaluation of long-range Coulombic interactions still represents a bottleneck in the molecular dynamics (MD) simulations of biological macromolecules. Despite the advent of sophisticated fast algorithms, such as the fast multipole method (FMM), accurate simulations still demand a great amount of computation time due to the accuracy/speed trade-off inherently involved in these algorithms. Unless higher order multipole expansions, which are extremely expensive to evaluate, are employed, a large amount of the execution time is still spent in directly calculating particle-particle interactions within the nearby region of each particle. To reduce this execution time for pair interactions, we developed a computation unit (board), called MD-Engine II, that calculates nonbonded pairwise interactions using a specially designed hardware. Four custom arithmetic-processors and a processor for memory manipulation ("particle processor") are mounted on the computation board. The arithmetic processors are responsible for calculation of the pair interactions. The particle processor plays a central role in realizing efficient cooperation with the FMM. The results of a series of 50-ps MD simulations of a protein-water system (50,764 atoms) indicated that a more stringent setting of accuracy in FMM computation, compared with those previously reported, was required for accurate simulations over long time periods. Such a level of accuracy was efficiently achieved using the cooperative calculations of the FMM and MD-Engine II. On an Alpha 21264 PC, the FMM computation at a moderate but tolerable level of accuracy was accelerated by a factor of 16.0 using three boards. At a high level of accuracy, the cooperative calculation achieved a 22.7-fold acceleration over the corresponding conventional FMM calculation. In the cooperative calculations of the FMM and MD-Engine II, it was possible to achieve more accurate computation at a comparable execution time by incorporating larger nearby regions.     

Computational studies of semiconductor quantum dots

Light-absorption and luminescence processes in nano-sized materials can be modelled either by using computational approaches developed for quantum chemical calculations or by applying computational methods in the effective mass approximation (EMA) originally intended for solid-state theory studies. An overview of the theory and implementation of an ab initio correlation EMA method for studies of luminescence properties of embedded semiconductor quantum dots is presented. The applicability of the method and the importance of correlation effects are demonstrated by calculations on InGaAs/GaAs quantum-dot and quantum-ring samples. Ab initio and density functional theory (DFT) quantum chemical studies of optical transitions in freestanding silicon nanoclusters are also discussed. The accuracy of the optical gaps and oscillator strengths for silicon nanoclusters obtained using different computational methods is addressed. Changes in the cluster structures, excitation energies and band strengths upon excitation are reported. The role of the surface termination and functional groups on the silicon nanocluster surfaces is discussed.     

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent

In molecular simulations with fixed-charge force fields, the choice of partial atomic charges influences numerous computed physical properties, including binding free energies. Many molecular mechanics force fields specify how nonbonded parameters should be determined, but various choices are often available for how these charges are to be determined for arbitrary small molecules. Here, we compute hydration free energies for a set of 44 small, neutral molecules in two different explicit water models (TIP3P and TIP4P-Ew) to examine the influence of charge model on agreement with experiment. Using the AMBER GAFF force field for nonbonded parameters, we test several different methods for obtaining partial atomic charges, including two fast methods exploiting semiempirical quantum calculations and methods deriving charges from the electrostatic potentials computed with several different levels of ab initio quantum calculations with and without a continuum reaction field treatment of solvent. We find that the best charge sets give a root-mean-square error from experiment of roughly 1 kcal/mol. Surprisingly, agreement with experimental hydration free energies does not increase substantially with increasing level of quantum theory, even when the quantum calculations are performed with a reaction field treatment to better model the aqueous phase. We also find that the semiempirical AM1-BCC method for computing charges works almost as well as any of the more computationally expensive ab initio methods and that the root-mean-square error reported here is similar to that for implicit solvent models reported in the literature. Further, we find that the discrepancy with experimental hydration free energies grows substantially with the polarity of the compound, as does its variation across theory levels.     

Molecular Modeling Study of Drug-DNA Combined to Single Walled Carbon Nanotube

One of the applications of nanotechnology is use of carbon nanotubes for the targeted delivery of drug molecules. To demonstrate the physical and chemical properties of biomolecules and identify new material of drug properties, the interaction of carbon nanotubes (CNTs) with biomolecules is a subject of many investigations. CNTs is a synthetic compound with extraordinary mechanical, thermal, electrical, optical, and chemical properties widely applied for technological purposes. In this article we have tried to investigate thermodynamic parameters and dielectric effects in different solvents for one of the most famous anticancer drug ??cisplatin?? combined to SWCNT, by Monte Carlo and density functional theory (DFT) calculations. Cause of platinum element in cisplatin we have done calculations as Gibbs free energy, thermal enthalpy, thermal energy and entropy at 6-31G** basis set with SCRF model of solvent. In this work, the major point has been embedded that results of both two methods of Monte Carlo and DFT can overlap with each other and cisplatin- SWCNT is a suitable compound for drug delivery in different media.     

Improved correlation energy extrapolation schemes based on local pair natural orbital methods

It is well-known that the basis set limit is difficult to reach in correlated post Hartree-Fock ab initio calculations. One possible route forward is to employ basis set extrapolation schemes. In order to avoid prohibitively expensive calculations, the highest level calculation (typically based on the "gold standard" coupled cluster theory with single, double, and perturbative triple excitations, CCSD(T)) is only performed with the smallest basis set, and the remaining basis set incompleteness is estimated at a lower level of theory, typically second-order M?ller-Plesset perturbation theory (MP2). In this work, we provide a comprehensive investigation of alternative schemes where the MP2 extrapolation is replaced by the coupled-electron pair approximation, version 1 (CEPA/1) or the local pair natural orbital version of this method (LPNO-CEPA/1). It is shown that the MP2 method achieves apparent accuracy only due to error cancellation. Systematically more accurate results at small additional computational cost are obtained if the MP2 step is replaced by LPNO-CEPA/1. The errors of LPNO-CEPA/1 relative to canonical CEPA/1 are negligible. Owing to the highly systematic nature of the deviations between canonical and LPNO methods, basis set extrapolation reduces the LPNO errors in the total energies by 1 order of magnitude (~0.2 kcal/mol) and errors in energy differences to essentially zero. Using the CCSD(T)/LPNO-CEPA/1-based extrapolation scheme, new reference values are proposed for the recently published S66 set of interaction energies. The deviations between the new values and the original interactions energies are mostly very small but reach values up to 0.3 kcal/mol.     

对含重元素体系的接合二分量-标量相对论密度泛函计算方法

在相对论密度泛函ZORA方法的基础上,提出一种用于含重元素体系的接合二分量-标量相对论密度泛函计算方法.对于只含少数几个重元素的较大体系,仅对其中旋轨耦合作用强的重元素作二分量相对论计算,而对体系的其余部分则作标量相对论计算,通过对动能矩阵元的近似处理实现两种计算的接合.对一系列含6p区重元素分子进行计算的结果表明,当非重元素是第三周期以前的元素时,此方法与二分量ZO-RA方法的计算结果吻合得很好.当非重元素为第四周期元素时,计算结果有一定偏差,表明在后一种情况下旋轨耦合作用已比较显著,但误差仍在目前近似密度泛函计算的精度范围内.此方法可以有效地节省计算量,而且避免了Dyall方法的缺点.     

Computation of large systems with an economic basis set: structures and reactivity indices of nucleic acid base pairs from density functional theory

We show here that an economic basis set can describe nucleic acid base pairs involving the hydrogen bond interactions in density functional calculations. The economic basis set in which the polarization function is added only to oxygen and nitrogen atoms of strong electronegativity can predict reliable geometric structures and dipole moment of nucleic acid base pairs, comparable to those obtained from the basis set of 6-31G* in B3LYP calculations. Combining single point calculations with the standard basis set on the geometric structures optimized by the economic basis set, the present approach has predicted accurate natural bond orbital charge, binding energy, electronegativity, hardness, softness, and electrophilicity index. The principle for basis selection presented in this study can be regarded as a general guideline in the computation of large biological systems with considerably high accuracy and low computational expense.     

Intracule densities in the strong-interaction limit of density functional theory

The correlation energy in density functional theory can be expressed exactly in terms of the change in the probability of finding two electrons at a given distance r(12) (intracule density) when the electron-electron interaction is multiplied by a real parameter lambda varying between 0 (Kohn-Sham system) and 1 (physical system). In this process, usually called adiabatic connection, the one-electron density is (ideally) kept fixed by a suitable local one-body potential. While an accurate intracule density of the physical system can only be obtained from expensive wavefunction-based calculations, being able to construct good models starting from Kohn-Sham ingredients would highly improve the accuracy of density functional calculations. To this purpose, we investigate the intracule density in the lambda --> infinity limit of the adiabatic connection. This strong-interaction limit of density functional theory turns out to be, like the opposite non-interacting Kohn-Sham limit, mathematically simple and can be entirely constructed from the knowledge of the one-electron density. We develop here the theoretical framework and, using accurate correlated one-electron densities, we calculate the intracule densities in the strong interaction limit for few atoms. Comparison of our results with the corresponding Kohn-Sham and physical quantities provides useful hints for building approximate intracule densities along the adiabatic connection of density functional theory.     

An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: application to alanine tetrapeptide conformational analysis

We present a new algorithm for analytical gradient evaluation in resolution‐of‐the‐identity second‐order Møller‐Plesset perturbation theory (RI‐MP2) and thoroughly assess its computational performance and chemical accuracy. This algorithm addresses the potential I/O bottlenecks associated with disk‐based storage and access of the RI‐MP2 t‐amplitudes by utilizing a semi‐direct batching approach and yields computational speed‐ups of approximately 2–3 over the best conventional MP2 analytical gradient algorithms. In addition, we attempt to provide a straightforward guide to performing reliable and cost‐efficient geometry optimizations at the RI‐MP2 level of theory. By computing relative atomization energies for the G3/99 set and optimizing a test set of 136 equilibrium molecular structures, we demonstrate that satisfactory relative accuracy and significant computational savings can be obtained using Pople‐style atomic orbital basis sets with the existing auxiliary basis expansions for RI‐MP2 computations. We also show that RI‐MP2 geometry optimizations reproduce molecular equilibrium structures with no significant deviations (>0.1 pm) from the predictions of conventional MP2 theory. As a chemical application, we computed the extended‐globular conformational energy gap in alanine tetrapeptide at the extrapolated RI‐MP2/cc‐pV(TQ)Z level as 2.884, 4.414, and 4.994 kcal/mol for structures optimized using the HF, DFT (B3LYP), and RI‐MP2 methodologies and the cc‐pVTZ basis set, respectively. These marked energetic discrepancies originate from differential intramolecular hydrogen bonding present in the globular conformation optimized at these levels of theory and clearly demonstrate the importance of long‐range correlation effects in polypeptide conformational analysis. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007