SOLVING THE SCHRODINGER EQUATION USING FUNDAMENTAL NUMERICAL PROCEDURES

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)SOLVING THE SCHRODINGER EQUATION USING FUNDAMENTAL NUMERICAL PROCEDURES. A combination of the variational principle, expectation value and Quantum Monte Carlo method is used to solve the Schrodinger equation for some simple systems. The results are accurate and the simplicity of this version of the Variational Quantum Monte Carlo method provides a powerful tool to teach alternative procedures and fundamental concepts in quantum chemistry courses. Some numerical procedures are described in order to control accuracy and computational efficiency. The method was applied to the ground state energies and a first attempt to obtain excited states is described.351020762082Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Clinical profile of patients diagnosed with tuberculosis treated at theUniversity Hospital of Londrina, Paraná

The objective of this study was to analyze the clinical profileof patients positive for tuberculosis through an epidemiological study, descriptive and retrospective, based on secondary data contained in medical records of patients that attended the Hospital Universitário de Londrina comprising from January 2010 to December 2014. From the medical records available for analysis at the moment of study 86 cases were positive for tuberculosis, being the majority male (65/76%) with age group comprised between 2 to 91 years. The main symptoms presented were cough (50/58%), fever (45/52%) and weight loss (34/40%). Regarding the clinical form, 58/67% of the patients presented the pulmonary form, and 28/33% the non-pulmonary form. Positive cases for tuberculosis in association with HIV/AIDS corresponded to 32/37%. Harmful habits were also reported in patients in which 30/34% were smokers, 20/23% drug users and 14/16% were alcoholics. Against scarcity of published data referring to tuberculosis in our region and its relevance to public health, our study contributes to the epidemiological aspects mainly in relation to the high number of cases of coinfection with Human ImmunodeficiencyVirus and patients with evolution to death, assisting the development and implementation of campaigns or projects aimed at early diagnosis and treatment

HOPX homeobox methylation in differentiated thyroid cancer and its clinical relevance

Background: The inactivation of the tumor-suppressor homeodomain-only protein X (HOPX) usually involves promoter methylation in several cancer types. This study aimed to investigate the HOPX-β mRNA expression and promoter methylation and their clinical relevance in differentiated thyroid cancer (DTC). Patients and methods: Clinicopathological data and paraffin-embedded thyroid tumor tissues from 21 patients with DTC and 6 with benign tumors (T) and their non-tumor parenchyma (NT) were investigated. Tumor cell lines (FTC238, FTC236 and WRO) were treated with demethylating agent. HOPX-β mRNA expression was assessed by qRT-PCR and methylation status by Q-MSP. Thyroid cancer data from Cancer Genome Atlas (TCGA) was also collected. Results: HOPX-β mRNA re-expression in two cell lines treated with demethylating agent was observed concomitantly with reduced promoter methylation. Reduced mRNA expression in T group compared to their NT was observed, and reduced protein expression in T compared to NT was observed in three cases. Low mRNA expression with high methylation status was detected in 6/14 DTC samples. High methylation status was associated with older age at diagnosis, recurrent or progressive disease and with the presence of new neoplasm event post initial therapy while hyper-methylation correlated with worse overall survival, worse disease-free status and older age. Conclusion: A moderate coupling of downregulation of HOPX-β mRNA expression in DTC followed by high HOPX-β promoter methylation was observed however; high HOPX promoter methylation status was associated with the worse prognosis of DTC patients

A Simplified Route To Obtain The Hartree And Hartree-fock Equations

Alternative considerably simpler ways of obtaining the Hartree and Hartree-Fock equations are presented. These alternatives do not replace the formal demonstrations, which should be introduced in undergraduate or graduate courses according to the required level of student training. However, the use of the present approaches allows a student-friendlier introduction of the basic principles of electronic structure calculations as a prior teaching resource to the formal demonstrations. General implications and comparisons between the Hartree and Hartree-Fock energies are discussed.387995100

G3(MP2)//B3-SBK : a revision of a composite theory for calculations of thermochemical properties including some non-transition elements beyond the fourth period

The method referred to as G3(MP2)//B3-SBK corresponds to an upgrade of the combination of the G3(MP2)//B3 theory with a compact effective pseudopotential (CEP), originally referred to as G3(MP2)//B3-CEP. The main modifications are related to: a) the replacement of Pople style basis functions by the respective 31G basis sets developed by Stevens, Basch and Krauss, b) re-optimization of the CEP-G3MP2large basis set with respect to some experimental data, c) re-optimization of the higher level correction (HLC) parameters, d) the use of scaled experimental atomization energies of the elements and e) the inclusion of conditions for the calculation of thermochemical properties considering molecules containing Sn and Sb. Evaluations were carried out with properties belonging to the G3/05 training set, i.e. enthalpies of formation, ionization energies, electron affinities, molecular atomization energies and proton affinities. The best combination of adjustments yielded a mean absolute error for all tested properties of 1.43 kcal mol(-1). This deviation is essentially equal to that presented by the all-electron G3(MP2)//B3 theory. The inclusion of 40 new molecules containing silicon (3 molecules), germanium (1 molecule), arsenic (4 molecules), tin (26 molecules), and antimony (6 molecules) to the G3/05 training set increased the mean absolute error for all calculated properties to 2.15 kcal mot(-1) using the conventional procedure and 1.86 kcal mor(-1) by including a scaling of the experimental atomization energies of the elements. Reference experimental properties with lower errors will provide better results for compounds containing Sn and Sb114917COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPnão tem2013/08293-7; 2017/11485-6The authors wish to thank Dr. Cleuton de Sousa Silva for helpful discussion and suggestions. We acknowledge financial support from FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo – Brazil - Center for Computational Engineering and Sciences, Grant 2013/08293-7, and Grant 2017/11485-6), and FAEPEX-UNICAMP (Fundo de Apoio ao Ensino, à Pesquisa e à Extensão da UNICAMP – Brazil). This study was also financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brazil (CAPES) - Finance Code 001. The National Center of High-Performance Computing in São Paulo (CENAPAD-SP) is acknowledged for access to their computational facilitie

Partial combination of composite strategy and the B3LYP functional for the calculation of enthalpies of formation

The B3LYP functional was re-optimized using partially composite methods for the calculation of standard enthalpies of formation. Two initial methods (B3LYP-MCM1 and B3LYP-MCM2) differing in the type and number of optimized parameters were analyzed using B3LYP/6-31+G(2df,p) as the reference energy. For the first method (B3LYP-MCM1), the exchange-correlation and higher-level correction parameters (HLC) were optimized and for the second method (B3LYP-MCM2), in addition to the previous parameters, scaling of the basis functions responsible for large errors in the enthalpy of formation were also optimized. The best parameters were also used as adapted functionals generating two other methods referred to as: B3LYP-MF1 and B3LYP-MF2. The best-performing results (B3LYP-MCM2 and B3LYP-MF2) presented mean absolute errors near 2.3kcalmol(-1) for the G3/05 test set. This is a significant improvement when compared with the respective results from B3LYP/6-31+G(2df,p), which yielded a mean absolute error of 5.3kcalmol(-1). The errors were larger for B3LYP-MCM1 (4.17kcalmol(-1)) and B3LYP-MF1 (3.98kcalmol(-1)). The scaling of the experimental atomization energies used for the calculation of enthalpy of formation was also tested for all four methods. This empirical adjustment reduced the errors to 2kcalmol(-1). The uncertainty of the best results with 95% confidence tended to be +/- 5.5kcalmol(-1). Substantial improvements were associated with the basis set adjustments253CAPES - Coordenação de Aperfeiçoamento de Pessoal e Nível SuperiorCNPQ - Conselho Nacional de Desenvolvimento Científico e TecnológicoFAPESP – Fundação de Amparo à Pesquisa Do Estado De São Paulosem informaçãosem informação2013/08293-7; 2017/11485-6FAPESP (Fundacao de Amparo a Pesquisa do Estado de Sao Paulo - Center for Computational Engineering and Sciences) [2013/08293-7, 2017/11485-6]; FAEPEX-UNICAMP (Fundo de Apoio ao Ensino, a Pesquisa e a Extensao da UNICAMP); Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior - Brasil (CAPES)CAPES [001]; CNPq (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico)National Council for Scientific and Technological Development (CNPq

Assessment of a composite method based on selected density functional theory methods and complete basis set extrapolation formulas

Extrapolation formulas based on power and exponential formulas, as well as alternatives from a Taylor series, were tested and used with density functional theory (DFT) for the calculation of enthalpies of formation. The following four functionals were analyzed: B3LYP, BMK, M06-2X, and B2PLYP. Preliminary tests pointed to B2PLYP and B3LYP as the best and worst functionals, respectively. Taylor series expressions were as accurate as the power formulas and presented better performance than the exponential equation. The power formula (Equation (2)) and one of the simplest Taylor expressions (Equation (13)) were selected for the calculations with B3LYP and B2PLYP, with further empirical adjustments based on the higher level correction (HLC) and scaling of the experimental atomization energies used to calculate enthalpies of formation. HLC improved the B3LYP mean absolute error (MAE) from approximately 4.3 to 3.5 kcal mol(-1) using both extrapolation alternatives. For B2PLY, the MAEs were improved from 2.7 to 2.6 kcal mol(-1). Regarding the G3/05 test set, a significant improvement in the MAEs around 2.5 and 1.5 kcal mol(-1) were achieved using B3LYP and B2PLYP, respectively. The accuracy obtained from these empirical corrections was equivalent to other composite methods. The MAEs from B3LYP and B2PLYP may be suggested as ranges for the possible accuracy to be achieved by some DFT methods. The empirical corrections suggested in this work are improvements that may be considered to provide acceptable accuracy for enthalpies of formation and possibly other properties11910CAPES - Coordenação de Aperfeiçoamento de Pessoal e Nível Superior0012013/08293‐7; 2017/11485‐

Policabornitrile: a semiemperical ab initio and de density functional study of molecular stability

2 p. : il., tabThe theoretical literature data with respectt o the electronic properties of this compound is quite scarce and makes use of the planar alltransStructure as the most stable for the calculations In this work semiempirical (AM1 and PM3), ab initio (at the Hartree-Fock level)and density functional theory (using the correlation functional of Vosko, Wilk and Nussair) were used to anaIyse the conformationalstability of the all-trans and all-cis dimers, t rimers and tetramers of polycarbonitrile.The semiempirical and ab initio calculations at theHartree-Fock level showed in general that the all-trans structure with respect to other conformers is the most unstable s tructure. TheInclusion of electronic correlation energy through t he MP2 calculations or the VWN functional method suggest that the trans structure isthe most stable. The relative energies calculated at the correlated level presented diferences around 2 kcal/mol among the differentconformers . While the all-cis compounds presented a planar structure for any of the three methods the all-trans polymer showed a strongdeviation of planarity with a set of local minima in its energy surface.These results suggestth that further calculations on the electronic properties of this polymer can be significantly different of those actually available in the literature

Theoretical study of the internal rotational barriers of fluorine, chlorine, bromine, and iodine-substituted ethanes

Physical and chemical characteristics of flexible compounds are extremely dependent of internal rotation barriers. On the other hand, halides of organic compounds are extremely common, and the nature of their rotation barriers are still poorly understood. As a simple example, the experimental height of the internal rotational barrier decreases with the number of fluorine-substituted in ethane, C2H5F, C2H4F2, and C2H3F3. For chlorinesubstituted ethane C2H5CI, C2H4Cl2 and C2H3Cl3 the internal rotational barrier converges in an opposite manner. No experimental results are available for the bromine- and iodine-substituted compounds C2H5Br, C2H4Br2, C2H3Br3, C2H5I, C2H4I2, and C2H3I3. In light of lack of both an adequate explanation for this phenomenon and experimental results for Br and I, the present work studied these compounds using different levels of theory: MP2, MP3, MP4, QCISD(T) and CCSD(T) methods, and the G3 and G3CEP composite theories. The results showed that the G3 and G3CEP theories were the most accurate calculations for the F- and Cl-substituted compounds as a result of the additive contributions of the energy values. From Natural Bond Orbitals (NBO), Quantum Theory of Atoms in Molecules (QTAIM) and Energy Decomposition Analysis (EDA) it was verified that the internal rotational barriers decrease with the addition of Fluorine atoms for fluorine-containing ethanes and can be explained by: pi character in the C-F bond and delocalization indexes (DI(A)) by QTAIM analysis; the interaction of the ligand and anti-ligand orbitals by NBO analysis and for the descriptors by EDA. On the other hand, the enlargement of the barriers with the addition of Cl, Br and I atoms for substituted ethanes, are dominated by the large electronic cloud of these halogens, which generates significant steric repulsion1166COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPnão tem2013/08293-7; 2017/11485-6The authors acknowledges the National Center for High Performance Processing (Centro Nacional de Processamento de Alto Desempenho – CENAPAD) in São Paulo, UNICAMP (Universidade de Campinas), for computational resources. The authors would like to thank FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo - Center for Computational Engineering and Sciences, Grant 2013/08293-7, and Grant 2017/11485-6). D.H. Pereira also acknowledges funding from CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Coordination of Improvement of Higher Education Personnel - Brazil), Funding Code 001 CAPES, and the UFT New Researchers Program (Programa Novos Pesquisadores da Universidade Federal do Tocantins - PROPESQ/UFT