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1

Counterion effects on the alkali dissolution mechanism of quartz

Yao Yu-yun, Tang Yun, Yang Yong, Li Guo-hui, Wu Bo, Dai Wen-zhi

Physicochemical Problems of Mineral Processing

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2023

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Vol. 59, iss. 1

art. no. 160038

EN

In gold ore, quartz plays an important role in mineral formation by acting as the follower. Understanding counterion release, transport, and deposition in alkali solution is a prerequisite for evaluating the potential role of gold separate from quartz deposits in pretreatment. In this work, the aggregation, retention, and release of counterion in alkali solution media were investigated by kinetic research and pure mineral experiments, the correlation and mechanism of these processes were revealed by combining geochemical theory, interaction energy calculation, and quantum chemistry. The results showed that the retention and release of counterion were closely related to the dissolution and corrosion rate of quartz. The NH4+ and Fe2+ with higher mineral affinity reduced the quartz stability, and the dispersion stability and mobility of the quartz were greatly improved by an alkaline substance due to the enhancement of steric hindrance effects. Quantum chemical calculation results show that ammonium ion promotes the dissolution of quartz stronger than ferrous ion, which is mainly reflected in reducing the activation energy required for the formation of transition state (TS1), which can be verified by kinetic calculation. These findings provide essential insight into the extraction of gold coated by quartz as well as a vital reference for the experiment of gold-loaded quartz leaching in mineral processing.

2

Do we still need a laboratory to study advanced oxidation processes? A review of the modelling of radical reactions used for water treatment

Wacławek Stanisław

Ecological Chemistry and Engineering. S

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2021

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Vol. 28, nr 1

11--28

EN

Environmental pollution due to humankind’s often irresponsible actions has become a serious concern in the last few decades. Numerous contaminants are anthropogenically produced and are being transformed in ecological systems, which creates pollutants with unknown chemical properties and toxicity. Such chemical pathways are usually examined in the laboratory, where hours are often needed to perform proper kinetic experiments and analytical procedures. Due to increased computing power, it becomes easier to use quantum chemistry computation approaches (QCC) for predicting reaction pathways, kinetics, and regioselectivity. This review paper presents QCC for describing the oxidative degradation of contaminants by advanced oxidation processes (AOP, i.e., techniques utilizing •OH for degradation of pollutants). Regioselectivity was discussed based on the Acid Blue 129 compound. Moreover, the forecasting of the mechanism of hydroxyl radical reaction with organic pollutants and the techniques of prediction of degradation kinetics was discussed. The reactions of •OH in various aqueous systems (explicit and implicit solvation) with water matrix constituents were reviewed. For example, possible singlet oxygen formation routes in the AOP systems were proposed. Furthermore, quantum chemical computation was shown to be an excellent tool for solving the controversies present in the field of environmental chemistry, such as the Fenton reaction debate [main species were determined to be: •OH < pH = 2.2 < oxoiron(IV)]. An ongoing discussion on such processes concerning similar reactions, e.g., associated with sulphate radical-based advanced oxidation processes (SR-AOP), could, in the future, be enriched by similar means. It can be concluded that, with the rapid growth of computational power, QCC can replace most of the experimental investigations related to the pollutant’s remediation in the future; at the same time, experiments could be pushed aside for quality assessment only.

3

Prediction of the Crystalline Densities of Aliphatic Nitrates by Quantum Chemistry Methods

Wang Guixiang, Xu Yimin, Xue Chuang, Ding Zhiyuan, Liu Yan, Liu Hui, Gong Xuedong

Central European Journal of Energetic Materials

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2019

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Vol. 16, no. 3

412--432

EN

Crystal density is a basic and important parameter for predicting the detonation performance of explosives, and nitrate esters are a type of compound widely used in the military context. In this study, thirty-one aliphatic nitrates were investigated using the density functional theory method (B3LYP) in combination with six basis sets (3-21G, 6-31G, 6-31G*, 6-31G**, 6-311G* and 6-31+G**) and the semiempirical molecular orbital method (PM3). Based on the geometric optimizations at various theoretical levels, the molecular volumes and densities were calculated. Compared with the available experimental data, the densities calculated by various methods are all overestimated, and the errors of the PM3 and B3LYP/3-21G methods are larger than those of other methods. Considering the results and the computer resources required by the calculations, the B3LYP/6-31G* method is recommended for predicting the crystalline densities of organic nitrates using a fitting equation. The results obtained with this method are slightly better than those reported by Keshavarz and Rice. In addition, the effects of various groups (such as –ONO2, –OH, –Cl, –O–, and –CH2–) on the densities are also discussed, which is helpful for the design of new molecules in terms of practical requirements.

4

Degradation mechanism study of amine collectors in Fenton process by quantitative structure-activity relationship analysis

Wang X., Liu W., Duan H., Liu W.

Physicochemical Problems of Mineral Processing

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2018

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Vol. 54, iss. 3

713--721

EN

In this study, advanced oxidation processes (AOPs), Fenton process, was applied to degrade ten amine collectors. The experimental results indicated that most of the tested amines could be removed rapidly and effectively at pH=4, while the degradation of quaternary ammonium compounds was less than others. To research the Fenton oxidation process, the degradation-rate constants of amine collectors were calculated by the pseudo-second order kinetic model, then which was used as the dependent variable to establish a quantitative structure activity relationship (QSAR) model. Meanwhile, 16 molecular structure descriptors and quantum mechanical parameters for amine collectors were simulated and analyzed by using Materials Studio software. The optimum QSAR model was established based on the partial least squares regression (PLS) method and confirmed by the statistics analysis. The model revealed that hydrogen bond acceptor (HBA) and the maximum values of electrophilic attack in C atom sites (f(-)c) were the major effect factors for the degradation-rate constants of amine collector.

5

Structure and separation quality of various N- and O-donor ligands from quantum-chemical calculations

Trumm M., Schimmelpfennig B., Geist A.

Nukleonika

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2015

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Vol. 60, No. 4, part 2

847--851

EN

Although BTP (2,6-di(1,2,4-triazin-3-yl)pyridine) has been proven to be a highly effective N-donor ligand for the selective An(III)/Ln(III) separation, the origin of its selectivity is still under discussion. We present in this paper quantum-chemical calculations at the density functional theory (DFT) and MP2 level which highlight the role of the aquo ions in the separation process. Furthermore these data will be the reference for future force-field development to investigate the differences in An(III) complexation reactions compared to their Ln(III) counterparts.

6

Quantum Chemical Study of Aminonitrocyclopentanes as Possible High Energy Density Materials (HEDMs)

Bai J., Chi W. J., Li L. L., Yan T., Wen X. E., Li B. T., Wu H. S., Ma F. L.

Central European Journal of Energetic Materials

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2013

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Vol. 10, no. 4

467--480

EN

Nitro and amine groups were introduced into the cyclopentane skeleton, and the heats of formation, detonation performance, bond dissociation energies, and impact sensitivity for these aminonitrocyclopentanes were calculated in detail at the B3LYP/6-311G** level. The results show that all of the derivatives have negative heats of formation, which are influenced by the position of the substituent groups. Their stabilities were estimated and analyzed according to their bond dissociation energies and calculated characteristic H50 values. Most of the compounds were found to have a lower impact sensitivity than HMX. Furthermore, the detonation velocities and detonation pressures were predicted via the Kamlet-Jacobs equation. Of all these aminonitrocyclopentanes, E has the best detonation properties (ρ = 2.05 g/cm3, D = 9.11 m/s, P = 39.62 GPa) and can be considered as a candidate high energy density material.

7

Quantum chemical study of organic inhibitors of corrosion and hydrogen absorption an investigation of the mechanism of bainite transformation in experimental 0.2c-1v-2mn steel

Beloglazov G.

Advances in Materials Science

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2012

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Vol. 12, nr 2(32)

5-18

EN

Results of quantum chemical calculations of the molecules of organic inhibitors (Oin) of corrosion and hydrogen absorption by metals (particularly, p-R-C6H4-SO2-NH2 where R= F, Cl, Br, CH3) both in free state and adsorbed on cluster modeling aluminium surface containing 20 atoms of Al are compared to experimental data on efficiencies of protective action (EPA) against corrosion by this metal. Energies of boundary orbitals (HOMO, LUMO) and dipole moments of isolated molecules of Oin as well as changes of atomic charges on Oin atoms when Oin molecule adsorbed have been computed using semi-empiric MNDO quantum chemistry method. It was found that correlation coefficients between EPA and changes of electric charge on N atom [?Q(N)] and O atom [?Q(O)] due to adsorption of Oin on the metal surface are the most significant. At adsorption and eventually the protection action of Oin, the specific role of polar groups (such as hydroxile) and specific role of heteroatoms (such as N, S etc) in the framework of the concepts of molecular orbitals and donor-acceptor interaction between adsorbent and adsorbate.

8

Tert-butyl esters of 2,3-diaryl-3-arylaminopropanoic acids – stereoselective synthesis, isolation, spectroscopic and structural elucidation

Tasheva D. N., Zareva S. Y.

Polish Journal of Chemical Technology

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2011

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Vol. 13, nr 3

12-17

EN

A series of seven substituted tert-butyl esters of 2,3-diaryl-3-arylaminopropanoic acids has been synthesized, isolated, spectroscopically and structurally elucidated. An influence of the substituents on the spectroscopic characteristics and conformations is discussed using the data of the linear-polarized IR- (IR-LD), UV-spectroscopy and 1H-NMR. Theoretical quantum chemical calculations are carried out, with a view to explaining and supporting the experimental optical properties and the electronic structure. The stereoselective synthesis of the corresponding diastereoisomers is optimized, thus giving good yields (62–72%) and purity of the compounds.

9

Grand challenges less challenging: new possibilities provided by Graphics Processing Units

Kuna D., Makowski M., Mazura G., Russek P., Janiszewski M., Wiatr K.

Bio-Algorithms and Med-Systems

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2011

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Vol. 7, no. 4

23--27

EN

The specific features of general-purpose computing on graphics processing units (GPGPU) in the area of scientific computing are highlighted. The hardware and software resources provided by CYFRONET are presented and selected benchmark calculations are briefly introduced.

10

FPGA implementation of exchange-correlation potential calculation for DFT

Wielgosz M., Jamro E., Russek P., Wiatr K.

Automatyka / Akademia Górniczo-Hutnicza im. Stanisława Staszica w Krakowie

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2011

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T. 15, z. 3

485-498

EN

Implementation results of the exchange-correlation module are presented in this paper. The authors have ported a computationally intensive part of quantum chemistry code to FPGA, which involved a substantial modification of its structure so that it matches the platform profile. Additionally, a set of the authors' customized modules for floating operations has been created along with software procedures handling FPGA-GPP intercommunication. Furthermore, several tests have been conducted to determine the speed-up achieved. Some more advanced computational cases have also been investigated to examine the module's performance increase with the number of atomic orbitals. The tests conducted for the orbital module revealed a significantly raised acceleration for higher atomic shells. This work also contains implementation results of the S matrix generation module, which are promising since the presented logic allows calculations to be conducted for 16 points simultaneously.

PL

W niniejszym artykule przedstawione zostały wyniki implementacji modułu obliczającego potencjał korelacyjno-wymienny dla procedury DFT. Autorzy zaimplementowali wymagające obliczeniowo fragmenty algorytmu DFT, co wiązało się ze znaczną modyfikacją algorytmu, tak by w pełni wykorzystać możliwości struktur rekonfigurowalnych. W konsekwencji powstał zestaw sprzętowych modułów zmiennoprzecinkowych oraz procedur zapewniających komunikacje pomiędzy częścią sprzętową oraz programowaną akceleratora. Przeprowadzone testy na platformie RASC wykazały przyspieszenie obliczeń wynoszące 3x dla modułu obliczającego wartość orbitalu atomowego w punkcie, natomiast większe przyspieszenie uzyskano dla jednostki realizujące obliczenia macierzy S.

11

Sprzętowa implementacja funkcji orbitalnej na potrzeby obliczeń kwantowo-chemicznych

Wielgosz M., Jamro E., Russek P., Wiatr K.

Pomiary Automatyka Kontrola

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2010

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R. 56, nr 7

705-707

PL

W niniejszym artykule przedstawione zostały wyniki implementacji modułu obliczającego wartość orbitalu atomowego w punkcie. Moduł ten stanowił cześć składową jednostki generującej wartość potencjału korelacyjno-wymiennego, wykorzystywaną w obliczeniach kwantowo-chemicznych. Prezentowana jednostka składa się z potokowych bloków zmiennoprzecinkowych. W pracy zaprezentowano również wyniki akceleracji obliczeń względem procesora ogólnego przeznaczenia Itanium2 1.6 GHz.

EN

The paper presents FPGA acceleration and implementation results of the orbital function calculation employed in quantum-chemistry. The orbital function core is composed of the authors' customized floating-point hardware modules. These modules are scalable from single to double precision, capable of working at frequency ranging from 100 to 200 MHz. Besides hardware implementation, the design process also involved reformulation of the algorithm in order to adapt them to the platform profile. The computational procedure presented in this paper is part of the algorithm for generating exchange-correlation potential, and is also recognized as one of the most computationally intensive routines. This feature justifies the effort devoted to develop its hardware implementation. The precision of floating-point operations becomes a primary concern when dealing with low-level quantum chemistry procedures, thus the authors have taken various measures to optimize them, both in terms of resource consumption and processing speed.

12

Sprzętowa implementacja części wielomianowej funkcji orbitalnej na potrzeby obliczeń kwantowo-chemicznych

Wielgosz M., Jamro E., Russek P., Wiatr K.

Automatyka / Akademia Górniczo-Hutnicza im. Stanisława Staszica w Krakowie

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2010

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T. 14, z. 3/2

939-949

PL

W artykule przedstawione zostały wyniki implementacji modułu obliczającego część wielomianową orbitalu atomowego. Generowanie funkcji orbitalnej jest jednym z najbardziej wymagających obliczeniowo fragmentów procedury DFT. Procedura ta wykorzystywana jest w chemii kwantowej do modelowania zaawansowanych wieloatomowych cząsteczek. Wykonanie obliczeń na komputerach dużej mocy zajmuje często wiele czasu, który dla bardziej skomplikowanych układów może wynosić nawet kilka dni. Dlatego została podjęta próba przyspieszenia obliczeń DFT z wykorzystaniem układów FPGA. Otrzymane wyniki akceleracji silnie zależą od charakteru cząsteczki, dla której prowadzone są obliczenia. Maksymalne uzyskane przyspieszenie wynosiło 3,5x. Należy oczekiwać większego przyspieszania, gdy kompletny algorytm generowania macierzy korelacyjno-wymiennej zostanie zaimplementowany w układzie FPGA.

EN

The hardware acceleration module for generating the polynomial part of the orbital function in quantum chemistry calculation is presented. Both implementation and acceleration results are provided in the paper along with the comparison tests (against Itanium 2 processor). The implementation described can be regarded as a milestone on the way towards introducing an efficient hardware implementation of the exchange-correlation potential. The FPGA-based SGI RASC accelerator was used to offload a processor in the most exhausting computations of the SCF routine. The paper also covers issues regarding an integration of the PP (polynomial part) module with the rest of the computational system.

13

Methods of theoretical description of molecular materials

Eilmes A.

Scientific Bulletin. Physics / Lodz University of Technology

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2006

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Vol. 26

13-19

EN

A review of some recent results in theoretical modeling of molecular materials is presented. Particular attention is paid to the possibility of developing complex models combining various theoretical approaches.

PL

w pracy omówiono podstawowe metody teoretyfcznego opisu/modelowania układów molekularnych: oblicznia ab initio, mechanika i dynamika molekularna, metody Monte Carlo. Przedstawiono przegląd najpopularniejszych programów i pakietów obliczeniowych. Zastosowanie metod obliczeniowych a takża potencjalne źródła problemów, jakie mogą się z nimi wiązać, zilustrowane zostały przykładami zaczerpniętymi z literatury (np. badania oligoacenów, modelowanie kryształów molekularnych) i z prac wykonywanych ostatnio w Zespole Półprzewodników Organicznych Wydziału Chemii UJ (np. parametryzacja oddziaływań międzycząsteczkowych i pól siłowych, modelowanie transportu jonów w stałym elektrolicie polimerowym).

14

Atomistic Studies of Fundamental Properties and Processes in Energetic Materials: Relevance to Mesoscale Initiation Phenomena

Sewell T. D.

Central European Journal of Energetic Materials

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2006

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Vol. 3, nr 1-2

19-38

EN

Genuine, physics-based understanding of initiation phenomena in plasticbonded explosives (PBXs) requires knowledge of the physics and chemistry at mesoscopic scales that are far larger than can be simulated directly using atomistic detail, yet far smaller than is directly resolvable in practical engineering scale continuum simulations. Initiation is determined by localization phenomena that arise due to the heterogeneous character of most explosive formulations. Indeed, the "average" temperature behind a weak shock is not a useful measure for understanding initiation phenomena; rather, it is the tails of the distributions in temperature, stress, and strain rates, localized to small, spatially distributed volumes in the material (hot spots), that dictate the outcome of a given loading event. Important factors for predicting hot spot formation and subsequent extinction or growth/coalescence include particle size, concentration, morphology, and void content; physical and chemical interactions between grains and binder; thermophysical and mechanical properties of the constituents and interfaces between them; and, of course, the inherent chemical stability of the explosive component(s) in the formulation. We are in the process of computing many of the thermophysical and mechanical properties required for a complete specification of constituent models for use in mesoscale simulations, wherein grains and binder in representative volumes of a PBX are spatially resolved and then studied within a continuum hydrodynamic framework. In addition to calculating specific properties of interest, we have recently undertaken a series of large-scale molecular dynamics simulations of energetic crystals to understand dissipation phenomena in dynamically loaded single- or poly-crystalline samples; for instance, plastic deformation and stress/energy localization mechanisms, phase transitions, and so on. Recent and ongoing work in these areas will be discussed, along with their specific relevance to emerging mesoscale simulation capabilities.

15

Polymerization of Vinyl Monomers on the High Disperse Aluminum-Containing Silica

Levytska S., Grebenyuk A., Brei V.

Polish Journal of Chemistry

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2003

|

Vol. 77 / nr 5

547-556

EN

The interaction of vinyl monomers (styrene, butyl vinyl ether, N-vinylpyrrolidinone, vinyltrimethylsilane, methyl acrylate, vinyl acetate, and vinylacetonitrile) vapours with aluminoaerosil surface has been studied by IR spectroscopy, thermal gravimetry, field ionization mass-spectrometry, and by quantum chemical simulations. The Bronsted acidic sites of the oxide (Í0 _ -3.0) were found to be capable to initiate an oligomerization of butyl-vinyl ether, styrene and N-vinylpyrrolidinone, whereas the monomers containing electron acceptor substituents (methyl acrylate, vinyl acetate, and vinylacetonitrile) are sorbed only in a physical way. The method of vapour phase oligomerization at temperatures 30-120_C has been shown to be a suitable way to produce disperse composite materials with a great content of organic matter (40-60 wt. %). Experimental and calculated absorption spectra support the idea on the formation of both monomeric and oligomeric protonated species due to adsorption of vinyl monomers on the surface of aluminum-containing silica unlike on that of pure silica.

16

Ab initio study of urea crystal

Xue D., Ratajczak H.

Bulletin of the Polish Academy of Sciences. Chemistry

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2003

|

Vol. 51, No. 3-4

143-153

EN

Dielectric properties - linear (refractive indices) and nonlinear optical responses - of urea crystal are quantitatively calculated using static ab initio quantum chemistry calculations at the self-consistent field (SCF) level of theory. The polarizabili-ties and first hyperpolarizabilities of the urea molecule are used to calculate macroscopic susceptibilities of the urea crystal. The calculated values of the urea crystal can agree well with experimental data and other reports. The effect of hydrogen bonds on the susceptibilities of the urea crystal may be neglected. The present work provides us a useful way to deal with quantum chemistry calculations of such molecular crystals as urea.

17

Kwantowochemiczne metody prognozowania selektywności [2 + 3] cykloaddycji

Jasiński Radomir, Markowska Agnieszka, Barański Andrzej

Wiadomości Chemiczne

|

2002

|

[Z] 56, 1-2

9--38

EN

In general, quantum-chemical methods for prediction of the outcome of cycloaddition reactions can be classified into three groups, depending on the particular reaction steps. The least used first group comprises the reactivity indexes, which are based on the analysis of stationary states of substrates. The second group contains the indirect methods of determination of activation energy, such as PMO, FMO and BL. The third group includes the methods relying on finding and characterization of critical structures on the corresponding potential energy hypersurface. BL and PMO methods can be applied only for the reactions that obey the principle of non-intercrossing of the energy profiles. These methods are mutually complementary and are used for description of different reaction stages of [2+3] cycloadditions. In the case of a late transition state, the activation energy is controlled primarily by the electronic effects related to formation of new bonds, rather than by the weak donor-acceptor interactions of substrates that are the basis for PMO and FMO methods. Reverse situation occurs when the activation barrier is controlled by an early transition state whose structure resembles substrates. Despite some reported successes, BL method has not become so popular as PMO. This results probably from the narrower scope of potential applications of the former method compared to the later one as well as from the BL method formalism. BL is used for explanation of specific aspects of [2+3] cycloadditions rather than for the reactivity predictions in the literal sense. Availability of fast computers and advanced quantum-chemical software has caused the [2+3] cycloaddition analysis based on localization and characterization of critical points on the potential energy hypersurface has gained popularity in recent years. Such analysis affords information about reactivity of the reagents, reaction mechanism, and, regio-, stereo- and periselectivity of practically any kind of reactions. By this method, transition state geometry and its physicochemical parameters, such as charge distribution, ionization potential, or dipole moment, can be determined. The transition state dipole moment can be used for prediction of the reaction course in solvents of different polarity. Moreover, there are procedures for direct calculations in the presence of a simulated dielectric medium, such as a solvent.

18

NANOPACK: parallel codes for semiempirical quantum-chemical calculations of large systems in the sp- and spd-basis

Berzigiyarov P. K., Zayets V. A., Ginzburg I. Ya., Razumov V. F., Sheka E. F.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

|

2002

|

Vol. 6, No 2

233-251

EN

A parallel implementation of the conventionally used NDDO (MNDO, AM1, PM3, CLUSTER-Z1) and modified NDDO-WF (CLUSTER-Z2) techniques for semiempirical quantum-chemical calculations on large molecular systems in the sp- and spd-basis, respectively, is described. The atom-pair distribution of data over processors forms the basis of the parallelization. The technological aspects of designing scalable parallel calculations on supercomputers (by using ScaLAPACK and MPI libraries) are discussed. The scaling of individual algorithms and entire package was carried out for model systems with 894, 1920, and 2014 atomic orbitals. The package speedup provided by different multi-processor systems involving a cluster of the Intel PIII processors, Alpha-21264-processor-built machine MBC-1000M, and CRAY-T3E, is analyzed. The effect of computer characteristics on the package performance is discussed.

19

Program package MP-ZAVA for parallel quantum-chemical computing in the spd-basis

Berzigiyarov P. K., Zayets V. A., Razumov V. F., Sheka E. F.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

|

2001

|

Vol. 5, No 3

271-300

EN

A parallel realization of the NDDO-WF technique for semi-empirical quantum-chemical calculations on large molecular systems in the spd-basis is described. The technological aspects of designing scalable parallel calculations on super computers (by using MPI library) are discussed. The scaling of individual algorithms and entire package was carried out for two model systems with a number of atomic orbitals of 894 and 2014, respectively. The speedup was determined in computer experiments with the RM600 E60 and Cluster Intel PIII multi-processor systems. The effect of communication rate on the package performance is discussed.

20

Quantum chemical studies of Cl-...HNO comlex in the singlet and triplet electronic states

Latajka Z., Ratajczak H.

Bulletin of the Polish Academy of Sciences. Chemistry

|

2001

|

Vol. 49, No. 2

125-131

EN

The structure and energetics of the hydrogen bonded complex formed between HNO and Cl- in the singlet and triplet states was investigated at the MP2 level with 6-31+ G(d, p) basis set. It is shown that the complex is strongly bound. The binding energy of the complex calculated at the MP4(SDTQ)/6-311++ G(2d,2p) level is -15.42 kcal/mol for the singlet state and —25.75 kcal/mol for the triplet state.