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1.
J Phys Chem A ; 128(36): 7634-7647, 2024 Sep 12.
Artículo en Inglés | MEDLINE | ID: mdl-39219502

RESUMEN

We analyze the structures, stabilities, and thermochemical properties of polyethylene (PE) oligomer chains cross-linked by metal (M) atoms through C-M-C bonds. Representative PEn-Mm-PEn complexes contain between 7 and 15 carbon atoms in each oligomer and one to three Li, Be, Mg, Zn, Ag, or Au cross-linking metal elements. PEn-Mm-PEn complexes are quasiplanar with nearly parallel PE chains. Their stability is determined by covalent C-M-C bonds accompanied by noncovalent dispersion interactions between PEn chains. Using the CAM-B3LYP+D3BJ+ABC functional, the binding energies of PE15-M-PE15 with respect to two PE15 radicals and metal fragments are -225, -230, -322, -551, -289, and -303 kJ/mol for Li, Ag, Au, Be, Mg, and Zn atoms, respectively. Entropy contributions (109 to 121 kJ/mol at 298.15 K) destabilize all complexes significantly. With two cross-linking metal elements in PE15-M2-PE15 complexes, binding energies are about double. Complexes with several open-shell Li, Ag, or Au doublet atoms have spins located on separated C-M-C bonds. High-spin PE15-Mm1-PE15-Mm2-PE15 complexes of three PE oligomers cross-linked by up to five doublet metal atoms create parallel PE tubes, which are suggested as elementary cells for modeling magnetic polymer tubes.

2.
J Chem Phys ; 160(17)2024 May 07.
Artículo en Inglés | MEDLINE | ID: mdl-38747994

RESUMEN

A proof-of-concept study is undertaken to demonstrate the utility of the machine learning combined with the thermodynamic perturbation theory (MLPT) to test the accuracy of electronic structure methods in finite-temperature thermodynamic calculations. As a test example, formic acid dimer is chosen, which is one of the systems included in the popular benchmark set S22 [Jurecka et al., Phys. Chem. Chem. Phys. 8, 1985-1993 (2006)]. Starting from the explicit molecular dynamics and thermodynamic integration performed at the PBE + D2 level, the MLPT is used to obtain fully anharmonic dimerization free and internal energies at the reference quality CCSD(T) level and 19 different density functional approximations, including GGA, meta-GGA, non-local, and hybrid functionals with and without dispersion corrections. Our finite-temperature results are shown to be both qualitatively and quantitatively different from those obtained using the conventional benchmarking strategy based on fixed structures. The hybrid functional HSE06 is identified as the best performing approximate method tested, with the errors in free and internal energies of dimerization being 36 and 41 meV, respectively.

3.
Cent Eur J Public Health ; 30(2): 86-92, 2022 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-35876596

RESUMEN

OBJECTIVES: Chemsex is a phenomenon highly relevant to public health concerns. Our primary aim is to describe the Czech chemsex scene regarding substances used, sexual behaviour, mental health, sexual life satisfaction, internalization of homonegative attitudes, and prevalent chemsex patterns. METHODS: The data from the European Men Who Have Sex With Men Internet Survey (EMIS) 2017 were used. The mental health of chemsex users was assessed by the Patient Health Questionnaire 4 (PHQ4), internalized homonegativity was measured using the Short Internalized Homonegativity Scale. A sample of 87 men who have sex with men (MSM) chemsex users and a comparison group of 261 MSM were selected from the total sample of 1,688 respondents. Mann-Whitney and χ2 tests were used to compare groups. RESULTS: Active chemsex users made up 5% of the sample (87 of 1,688), with an average age of 37 years. Chemsex users were more likely to engage in condomless sex with non-steady partners (χ2 = 46.8, p < 0.001), and had dramatically more STIs, such as HIV (χ2 = 52.9, p < 0.001), HCV (χ2 = 25.9, p < 0.001), and syphilis (χ2 = 41.5, p < 0.001). Chemsex users frequently injected drugs (n = 19, 20%). More than half (n = 48; 55%) of chemsex users had sober sex in the last 4 weeks. Chemsex culture was associated with riskier substance use, both in terms of mode and frequency. The mental health of chemsex users in our sample did not differ significantly from the comparison group (χ2 = 0.2, p < 0.7). Chemsex users did not conceal their sexual identity more often than the comparison group, on the contrary, 69% (n = 59) of them were out to most significant others, compared to 53% (n = 134) in the comparison group (χ2 = 8.8, p < 0.05). In addition, we did not find differences in the degree of internalized homonegativity (χ2 = 0.9, p < 0.4). Chemsex users were clearly and significantly more satisfied with their sex life than the comparison group (Mann-Whitney U test, p < 0.001). CONCLUSIONS: In our sample, chemsex use was not associated with a negative impact on health or wellbeing. Our results suggest that chemsex is not a homogeneous phenomenon. Many different patterns and subcultures exist, some of them are riskier, some safer than others.


Asunto(s)
Minorías Sexuales y de Género , Trastornos Relacionados con Sustancias , Adulto , República Checa/epidemiología , Homosexualidad Masculina , Humanos , Masculino , Conducta Sexual/psicología , Trastornos Relacionados con Sustancias/epidemiología , Encuestas y Cuestionarios , Sexo Inseguro
4.
J Phys Chem A ; 125(26): 5819-5828, 2021 Jul 08.
Artículo en Inglés | MEDLINE | ID: mdl-34180661

RESUMEN

The structures, vibrational frequencies, and model IR spectra of the monohydrates of oxygenated mercury compounds (BrHgO, BrHgOH, BrHgOOH, BrHgNO2, BrHgONO, and HgOH) have been theoretically studied using the ωB97X-D/aug-cc-pVTZ level of theory. The ground state potential energy surface exhibits several stable structures of these monohydrates. The thermodynamic properties of the hydration reactions have been calculated at different levels of theory including DFT and coupled-cluster calculations DK-CCSD(T) with the ANO-RCC-Large basis sets. Standard enthalpies and Gibbs free energies of hydration were computed. The temperature dependence of ΔrG°(T) was evaluated for the most stable complexes over the temperature range 200-400 K. Thermodynamic data revealed that the highest fraction hydrated at 298 K and 100% relative humidity will be BrHgNO2-H2O at ∼5%.

5.
J Chem Phys ; 146(10): 104304, 2017 Mar 14.
Artículo en Inglés | MEDLINE | ID: mdl-28298123

RESUMEN

Correlated ab initio methods (CASPT2 and CCSD(T)) in conjunction with the ANO-RCC basis sets were used to calculate potential energy curves (PECs) of the ground, valence, and Rydberg electronic states of CsH with the inclusion of the scalar relativistic effects. The spectroscopic constants of bound states were calculated from the PECs and compared with previous theoretical and/or available experimental data. Absorption and emission spectra arising from the transition between X1Σ+ and A1Σ+ states were modelled using vibrational and rotational energy levels and corresponding nuclear wave functions obtained via the direct numerical integration of one-dimensional rovibrational Schrödinger equation in the CASPT2/ANO-RCC electronic potentials. The anharmonic shape of the A1Σ+ potential and the shape of the pertinent vibrational wave functions have an interesting impact on the final shape of the spectrum and result in the complicated fine structure of individual emission bands.

6.
Euro Surveill ; 22(48)2017 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-29208160

RESUMEN

Reported incidence of human immunodeficiency virus (HIV) infection in the Czech Republic increased steeply over the past decade from 90 new cases in 2005 to 266 in 2015. This increase is almost exclusively attributed to sexual transmissions between men who have sex with men (MSM). In 2015, there were 79% (n=210) newly diagnosed cases among MSM, 17% (n=45) were attributed to heterosexual transmission and 1% (n=3) to people who inject drugs. Interventions targeted at MSM have not yet been prioritised in the broadly focused national HIV prevention strategy which this is envisaged to change in the programme set out for 2018 to 2022. The national budget for HIV prevention has been reduced, however, and this remains. Availability of voluntary counselling and testing has decreased substantially in the past decade. Post- and pre-exposure prophylaxis for sexual intercourse among MSM are not part of the HIV prevention policy and the concept of treatment as prevention is not fully recognised. Provision of a combined prevention strategy with a focus on MSM, reflecting the above factors including stigmatisation, should contribute to reverse the development of a concentrated HIV epidemic among MSM in the Czech Republic.


Asunto(s)
Antirretrovirales/administración & dosificación , Epidemias , Infecciones por VIH/epidemiología , Homosexualidad Masculina , Profilaxis Posexposición , Profilaxis Pre-Exposición , Adulto , República Checa/epidemiología , Infecciones por VIH/diagnóstico , Infecciones por VIH/prevención & control , Infecciones por VIH/transmisión , Conocimientos, Actitudes y Práctica en Salud , Política de Salud , Humanos , Masculino , Tamizaje Masivo
8.
Int J Health Geogr ; 13: 41, 2014 Oct 14.
Artículo en Inglés | MEDLINE | ID: mdl-25316603

RESUMEN

BACKGROUND: A youths' neighborhood can play an important role in their physical, health, and emotional development. The prevalence of health risk behavior (HRB) in Czech youth such as smoking, drug and alcohol use is the highest in Europe. AIM: To analyze differences in HRB in youth residents within different types of Prague's neighborhoods in relation to the perception of the built environment, quality of their school and home environments. DATA AND METHODS: The data is based on the on-line survey among elementary school students aged between 14-15 years, which was administered in19 selected schools in Prague, during the months of October 2013 to March 2014. Respondents were asked their opinions on various issues related to their HRB, about their indoor and outdoor housing and school environments. The questionnaire was completed by 407 students. Factor analysis with a principal components extraction was applied to determine the underlying structure in the variables. A consequent field research was conducted to map the opportunity hot spots and critical places around the elementary schools. RESULTS: Binge drinking has been reported mainly by the students living in the housing estates with blocks of flats. The most frequent occurrence of daily smokers was found in the neighborhoods of old city apartment houses. High prevalence of risky marijuana use almost in all the surveyed types of neighborhoods. The respondents were more critical in their evaluation of school characteristics. The neighborhoods critically evaluated by the students as regards the school outdoor environments were the older apartment houses in the historical centre and inner city, the school indoor environment was worst assessed within the housing estate neighborhoods. CONCLUSIONS: Our results suggest that perceptions of problems in both residential and school environment are associated with HRB. This fact makes this issue of a serious importance also from the policy point of view. Mainly the school surroundings have to be better managed by the local authorities responsible for the public space. This research thus forms part of the Sophie project aiming to find the most efficient policies that would tackle with the inequalities in the health and quality of life.


Asunto(s)
Comunismo , Ambiente , Conductas Relacionadas con la Salud/etnología , Características de la Residencia , Asunción de Riesgos , Población Urbana , Adolescente , Consumo de Bebidas Alcohólicas/etnología , Consumo de Bebidas Alcohólicas/psicología , Comunismo/estadística & datos numéricos , República Checa/etnología , Recolección de Datos/métodos , Femenino , Humanos , Masculino , Fumar Marihuana/etnología , Fumar Marihuana/psicología , Proyectos Piloto , Características de la Residencia/estadística & datos numéricos , Fumar/etnología , Fumar/psicología , Población Urbana/estadística & datos numéricos
9.
Epidemiol Psychiatr Sci ; 33: e16, 2024 Mar 21.
Artículo en Inglés | MEDLINE | ID: mdl-38511544

RESUMEN

AIMS: The mental health of sexual minority (SM) individuals remains overlooked and understudied in Czechia. We aimed to estimate (1) the prevalence rate and (2) the relative risk of common mental disorders and (3) the mental distress severity among the Czech SM people compared with the heterosexual population. In addition, we aimed to investigate help-seeking for mental disorders in SM people. METHODS: We used data from a cross-sectional, nationally representative survey of Czech community-dwelling adults, consisting of 3063 respondents (response rate = 58.62%). We used the Mini-International Neuropsychiatric Interview to assess the presence of mental disorders. In individuals scoring positively, we established help-seeking in the past 12 months. We assessed symptom severity using the 9-item Patient Health Questionnaire and the 7-item Generalized Anxiety Disorder scale. We computed the prevalence of mental disorders and the treatment gap with 95% confidence intervals. To assess the risk of having a mental disorder, we used binary logistic regression. RESULTS: We demonstrated that the prevalence of current mental disorders was 18.85% (17.43-20.28), 52.27% (36.91-67.63), 33.33% (19.5-47.17) and 25.93% (13.85-38) in heterosexual, gay or lesbian, bisexual and more sexually diverse individuals, respectively. Suicidal thoughts and behaviours were present in 5.73% (4.88-6.57), 25.00% (11.68-38.32), 22.92% (10.58-35.25) and 11.11% (2.45-19.77) of heterosexual, gay or lesbian, bisexual and more sexually diverse individuals, respectively. After confounder adjustment, gay or lesbian individuals were more likely to have at least one current mental disorder compared with heterosexual counterparts (odds ratio = 3.51; 1.83-6.76). For bisexual and sexually more diverse individuals, the results were consistent with a null effect (1.85; 0.96-3.45 and 0.89; 0.42-1.73). The mean depression symptom severity was 2.96 (2.81-3.11) in heterosexual people and 4.68 (2.95-6.42), 7.12 (5.07-9.18) and 5.17 (3.38-6.95) in gay or lesbian, bisexual and more sexually diverse individuals, respectively. The mean anxiety symptom severity was 1.97 (1.85-2.08) in heterosexual people and 3.5 (1.98-5.02), 4.63 (3.05-6.2) and 3.7 (2.29-5.11) in gay or lesbian, bisexual and more sexually diverse individuals, respectively. We demonstrated broadly consistent levels of treatment gap in heterosexual and SM individuals scoring positively for at least one current mental disorder (82.91%; 79.5-85.96 vs. 81.13%; 68.03-90.56). CONCLUSIONS: We provide evidence that SM people in Czechia have substantially worse mental health outcomes than their heterosexual counterparts. Systemic changes are imperative to provide not only better and more sensitive care to SM individuals but also to address structural stigma contributing to these health disparities.


Asunto(s)
Homosexualidad Femenina , Minorías Sexuales y de Género , Adulto , Femenino , Humanos , Estudios Transversales , Salud Mental , República Checa/epidemiología
10.
J Phys Chem B ; 128(20): 4943-4951, 2024 May 23.
Artículo en Inglés | MEDLINE | ID: mdl-38733335

RESUMEN

Options to improve the extrapolation power of the neural network designed using the SchNetPack package with respect to top docking scores prediction are presented. It is shown that hyperparameter tuning of the atomistic model representation (in the schnetpack.representation) improves the prediction of the top scoring compounds, which have characteristically a low incidence in randomized data sets for training of machine learning models. The prediction robustness is evaluated according to the mean square error (MSE) and the entropy of the average loss landscape decrease. Admittedly, the improvement of the top scoring compounds' prediction accuracy comes with the penalty of worsening the overall prediction power. It is revealed that the most impactful hyperparameter is the cutoff (5 Å is reported as the optimal choice). Other parameters (e.g., number of radial basis functions, number of interaction layers of the neural network, feature vector size or its batch size) are found to not affect the prediction robustness of the top scoring compounds in any comparable way relative to the cutoff. The MSE of the best docking score prediction (below -13 kcal/mol) improves from ca. 3.5 to 0.9 kcal/mol, while the prediction of less potent compounds (-13 to -11 kcal/mol) shows a lesser improvement, i.e., a decrease of MSE from 1.6 to 1.3 kcal/mol. Additionally, oversampling and undersampling of the training set with respect to the top scoring compounds' abundance is presented. The results indicate that the cutoff choice performs better than over- or undersampling of the training set, with undersampling performing better than oversampling.

11.
Chemphyschem ; 14(4): 698-707, 2013 Mar 18.
Artículo en Inglés | MEDLINE | ID: mdl-23315749

RESUMEN

The performance of the second-order Møller-Plesset perturbation theory MP2.5 and MP2.X methods, tested on the S22, S66, X40, and other benchmark datasets is briefly reviewed. It is found that both methods produce highly accurate binding energies for the complexes contained in these data sets. Both methods also provide reliable potential energy curves for the complexes in the S66 set. Among the routinely used wavefunction methods, the only other technique that consistently produces lower errors, both for stabilization energies and geometry scans, is the spin-component-scaled coupled-clusters method covering iterative single- and double-electron excitations, which is, however, substantially more computationally intensive. The structures originated from full geometrical gradient optimizations at the MP2.5 and MP2.X level of theory were confirmed to be the closest to the CCSD(T)/CBS (coupled clusters covering iterative single- and double-electron excitations and perturbative triple-electron excitations performed at the complete basis set limit) geometries among all the tested methods (e.g. MP3, SCS(MI)-MP2, MP2, M06-2X, and DFT-D method evaluated with the TPSS functional). The MP2.5 geometries for the tested complexes deviate from the references almost negligibly. Inclusion of the scaled third-order correlation energy results in a substantial improvement of the ability to accurately describe noncovalent interactions. The results shown here serve to support the notion that MP2.5 and MP2.X are reasonable alternative methods for benchmark calculations in cases where system size or (lack of) computational resources preclude the use of CCSD(T)/CBS computations. MP2.X allows for the use of smaller basis sets (i.e. 6-31G*) with results that are nearly identical to those of MP2.5 with larger basis sets, which dramatically decreases computation times and makes calculations on much larger systems possible.


Asunto(s)
Teoría Cuántica
12.
Biophys Chem ; 288: 106854, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-35810518

RESUMEN

Molecular docking of 234 unique compounds identified in the softwood bark (W set) is presented with a focus on their inhibition potential to the main protease of the SARS-CoV-2 virus 3CLpro (6WQF). The docking results are compared with the docking results of 866 COVID19-related compounds (S set). Furthermore, machine learning (ML) prediction of docking scores of the W set is presented using the S set trained TensorFlow, XGBoost, and SchNetPack ML approaches. Docking scores are evaluated with the Autodock 4.2.6 software. Four compounds in the W set achieve a docking score below -13 kcal/mol, with (+)-lariciresinol 9'-p-coumarate (CID 11497085) achieving the best docking score (-15 kcal/mol) within the W and S sets. In addition, 50% of W set docking scores are found below -8 kcal/mol and 25% below -10 kcal/mol. Therefore, the compounds identified in the softwood bark, show potential for antiviral activity upon extraction or further derivatization. The W set molecular docking studies are validated by means of molecular dynamics (five best compounds). The solubility (Log S, ESOL) and druglikeness of the best docking compounds in S and W sets are compared to evaluate the pharmacological potential of compounds identified in softwood bark.


Asunto(s)
COVID-19 , SARS-CoV-2 , Antivirales/farmacología , Aprendizaje Automático , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Péptido Hidrolasas , Corteza de la Planta , Inhibidores de Proteasas/farmacología
13.
Comput Biol Chem ; 98: 107656, 2022 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-35288359

RESUMEN

Molecular docking results of two training sets containing 866 and 8,696 compounds were used to train three different machine learning (ML) approaches. Neural network approaches according to Keras and TensorFlow libraries and the gradient boosted decision trees approach of XGBoost were used with DScribe's Smooth Overlap of Atomic Positions molecular descriptors. In addition, neural networks using the SchNetPack library and descriptors were used. The ML performance was tested on three different sets, including compounds for future organic synthesis. The final evaluation of the ML predicted docking scores was based on the ZINC in vivo set, from which 1,200 compounds were randomly selected with respect to their size. The results obtained showed a consistent ML prediction capability of docking scores, and even though compounds with more than 60 atoms were found slightly overestimated they remain valid for a subsequent evaluation of their drug repurposing suitability.


Asunto(s)
COVID-19 , SARS-CoV-2 , Antivirales/uso terapéutico , Humanos , Aprendizaje Automático , Simulación del Acoplamiento Molecular , Inhibidores de Proteasas
14.
J Abnorm Psychol ; 130(7): 713-726, 2021 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-34780228

RESUMEN

Sexual minority men are at greater risk of depression and suicidality than heterosexuals. Stigma, the most frequently hypothesized risk factor for this disparity, operates across socioecological levels-structural (e.g., laws), interpersonal (e.g., discrimination), and individual (e.g., self-stigma). Although the literature on stigma and mental health has focused on interpersonal and individual forms of stigma, emerging research has shown that structural stigma is also associated with adverse mental health outcomes. However, there is limited data on whether changes in structural stigma, such as when a stigmatized person moves to a lower stigma context, affect mental health, and on the mechanisms underlying this association. To address these questions, we use data from the 2017/18 European Men-who-have-sex-with-men Internet Survey (n = 123,428), which assessed mental health (i.e., Patient Health Questionnaire) and psychosocial mediators (i.e., sexual orientation concealment, internalized homonegativity, and social isolation). We linked these data to an objective indicator of structural stigma related to sexual orientation-including 15 laws and policies as well as aggregated social attitudes-in respondents' countries of origin (N = 178) and receiving countries (N = 48). Among respondents who still live in their country of birth (N = 106,883), structural stigma was related to depression and suicidality via internalized homonegativity and social isolation. Among respondents who moved from higher-to-lower structural stigma countries (n = 11,831), longer exposure to the lower structural stigma environments of their receiving countries was associated with a significantly: 1) lower risk of depression and suicidality; 2) lower odds of concealment, internalized homonegativity, and social isolation; and 3) smaller indirect effect of structural stigma on mental health through these mediators. This study provides additional evidence that stigma is a sociocultural determinant of mental health. (PsycInfo Database Record (c) 2021 APA, all rights reserved).


Asunto(s)
Depresión , Homosexualidad Masculina , Estigma Social , Suicidio , Depresión/epidemiología , Salud Global/estadística & datos numéricos , Homosexualidad Masculina/psicología , Homosexualidad Masculina/estadística & datos numéricos , Humanos , Masculino , Análisis Multinivel , Suicidio/psicología
15.
J Comput Chem ; 31(1): 224-47, 2010 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-19499541

RESUMEN

Some of the new unique features of the MOLCAS quantum chemistry package version 7 are presented in this report. In particular, the Cholesky decomposition method applied to some quantum chemical methods is described. This approach is used both in the context of a straight forward approximation of the two-electron integrals and in the generation of so-called auxiliary basis sets. The article describes how the method is implemented for most known wave functions models: self-consistent field, density functional theory, 2nd order perturbation theory, complete-active space self-consistent field multiconfigurational reference 2nd order perturbation theory, and coupled-cluster methods. The report further elaborates on the implementation of a restricted-active space self-consistent field reference function in conjunction with 2nd order perturbation theory. The average atomic natural orbital basis for relativistic calculations, covering the whole periodic table, are described and associated unique properties are demonstrated. Furthermore, the use of the arbitrary order Douglas-Kroll-Hess transformation for one-component relativistic calculations and its implementation are discussed. This section especially focuses on the implementation of the so-called picture-change-free atomic orbital property integrals. Moreover, the ElectroStatic Potential Fitted scheme, a version of a quantum mechanics/molecular mechanics hybrid method implemented in MOLCAS, is described and discussed. Finally, the report discusses the use of the MOLCAS package for advanced studies of photo chemical phenomena and the usefulness of the algorithms for constrained geometry optimization in MOLCAS in association with such studies.


Asunto(s)
Algoritmos , Teoría Cuántica , Programas Informáticos , Fotoquímica/métodos
16.
Phys Chem Chem Phys ; 12(33): 9611-4, 2010 Sep 07.
Artículo en Inglés | MEDLINE | ID: mdl-20623085

RESUMEN

The same- and opposite-spin scaling parameters for the SCS-CCSD method were reparametrized on the basis of benchmark CCSD(T)/CBS set interaction energies from the S22 set. New parameters were close to the original ones but swap between the different spin components, being 1.11 for the opposite- and 1.28 for the same-spin component. The RMSD, and especially, the largest error for the S22 were significantly reduced in comparison with the original parametrization. These statistical factors were only slightly worse when the S22x5 test set, containing not only the equilibrium but also the non-equilibrium geometries, was used. This new method, named the SCS(MI)-CCSD ("MI" stands for "Molecular Interactions") can thus be recommended for highly accurate calculations of interaction energies of various noncovalent interaction types, for which the CCSD(T)/CBS calculations are impractical.


Asunto(s)
Modelos Químicos , Enlace de Hidrógeno , Termodinámica
17.
Chemphyschem ; 10(1): 282-9, 2009 Jan 12.
Artículo en Inglés | MEDLINE | ID: mdl-19115327

RESUMEN

Scaled MP3 interaction energies calculated as a sum of MP2/CBS (complete basis set limit) interaction energies and scaled third-order energy contributions obtained in small or medium size basis sets agree very closely with the estimated CCSD(T)/CBS interaction energies for the 22 H-bonded, dispersion-controlled and mixed non-covalent complexes from the S22 data set. Performance of this so-called MP2.5 (third-order scaling factor of 0.5) method has also been tested for 33 nucleic acid base pairs and two stacked conformers of porphine dimer. In all the test cases, performance of the MP2.5 method was shown to be superior to the scaled spin-component MP2 based methods, e.g. SCS-MP2, SCSN-MP2 and SCS(MI)-MP2. In particular, a very balanced treatment of hydrogen-bonded compared to stacked complexes is achieved with MP2.5. The main advantage of the approach is that it employs only a single empirical parameter and is thus biased by two rigorously defined, asymptotically correct ab-initio methods, MP2 and MP3. The method is proposed as an accurate but computationally feasible alternative to CCSD(T) for the computation of the properties of various kinds of non-covalently bound systems.


Asunto(s)
Modelos Químicos , Nucleótidos/química , Algoritmos , Enlace de Hidrógeno , Termodinámica
18.
J Comput Chem ; 29(6): 861-70, 2008 Apr 30.
Artículo en Inglés | MEDLINE | ID: mdl-17963233

RESUMEN

Correlated ab initio calculations on large systems, such as the popular MP2 (or RI-MP2) method, suffer from the intramolecular basis set superposition error (BSSE). This error is typically manifested in molecules with folded structures, characterized by intramolecular dispersion interactions. It can dramatically affect the energy differences between various conformers as well as intramolecular stabilities, and it can even impair the accuracy of the predictions of the equilibrium molecular structures. In this study, we will present two extreme cases of intramolecular BSSE, the internal stability of [n]helicene molecules and the relative energies of various conformers of phenylalanyl-glycyl-phenylalanine tripeptide (Phe-Gly-Phe), and compare the calculated data with benchmark values (experimental or high-level theoretical data). As a practical and cheap solution to the accurate treatment of the systems with large anticipated value of intramolecular BSSE, the recently developed density functional method augmented with an empirical dispersion term (DFT-D) is proposed and shown to provide very good results in both of the above described representative cases.


Asunto(s)
Péptidos/química , Compuestos Policíclicos/química , Glicina/química , Modelos Químicos , Modelos Moleculares , Conformación Molecular , Fenilalanina/química , Teoría Cuántica , Termodinámica
19.
Chemphyschem ; 9(11): 1636-44, 2008 Aug 04.
Artículo en Inglés | MEDLINE | ID: mdl-18574830

RESUMEN

The CCSD(T) interaction energies for the H-bonded and stacked structures of the uracil dimer are determined at the aug-cc-pVDZ and aug-cc-pVTZ levels. On the basis of these calculations we can construct the CCSD(T) interaction energies at the complete basis set (CBS) limit. The most accurate energies, based either on direct extrapolation of the CCSD(T) correlation energies obtained with the aug-cc-pVDZ and aug-cc-pVTZ basis sets or on the sum of extrapolated MP2 interaction energies (from aug-cc-pVTZ and aug-cc-pVQZ basis sets) and extrapolated DeltaCCSD(T) correction terms [difference between CCSD(T) and MP2 interaction energies] differ only slightly, which demonstrates the reliability and robustness of both techniques. The latter values, which represent new standards for the H-bonding and stacking structures of the uracil dimer, differ from the previously published data for the S22 set by a small amount. This suggests that interaction energies of the S22 set are generated with chemical accuracy. The most accurate CCSD(T)/CBS interaction energies are compared with interaction energies obtained from various computational procedures, namely the SCS-MP2 (SCS: spin-component-scaled), SCS(MI)-MP2 (MI: molecular interaction), MP3, dispersion-augmented DFT (DFT-D), M06-2X, and DFT-SAPT (SAPT: symmetry-adapted perturbation theory) methods. Among these techniques, the best results are obtained with the SCS(MI)-MP2 method. Remarkably good binding energies are also obtained with the DFT-SAPT method. Both DFT techniques tested yield similarly good interaction energies. The large magnitude of the stacking energy for the uracil dimer, compared to that of the benzene dimer, is explained by attractive electrostatic interactions present in the stacked uracil dimer. These interactions force both subsystems to approach each other and the dispersion energy benefits from a shorter intersystem separation.


Asunto(s)
Uracilo/química , Algoritmos , Benceno/química , Dimerización , Transferencia de Energía , Enlace de Hidrógeno , Modelos Químicos
20.
J Phys Chem A ; 112(30): 7115-23, 2008 Jul 31.
Artículo en Inglés | MEDLINE | ID: mdl-18593134

RESUMEN

Interaction energies of the model H-bonded complexes, the formamide and formamidine dimers, as well as the stacked formaldehyde and ethylene dimers are calculated by the coupled cluster CCSD(T) method. These systems serve as a model for H-bonded and stacking interactions, typical in molecules participating in biological systems. We use the optimized virtual orbital space (OVOS) technique, by which the dimension of the space of virtual orbitals in coupled cluster CCSD(T) calculations can be significantly reduced. We demonstrate that when the space of virtual orbitals is reduced to 50% of the full space, which means reducing computational demands by 1 order of magnitude, the interaction energies for both H-bonded and stacked dimers are affected by no more than 0.1 kcal/mol. This error is much smaller than the error when interaction energies are calculated using limited basis sets.

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