Pub Date : 2007-11-01DOI: 10.1163/157404007782913138
V. Ludwig, S. Canuto
A combined and sequential Monte Carlo/quantum mechanics methodology is used to estimate the dipole polarizability of uracil in aqueous solution in normal thermodynamic conditions. Using the structures generated by the MC simulation, statistically uncorrelated configurations are sampled for subsequent quantum mechanical calculations using the central uracil molecule surrounded by the first solvation shell composed of 26 explicit water molecules. The dipole polarizability is obtained as an average value obtained from density-functional-theory calculations, using the B3P86 functional with varying basis sets. Statistically convergent result for the dipole polarizability of uracil in aqueous solution gives the average value of 100.1 ± 10.4 a03, indicating an increase of about 50% compared to the gas phase result.
{"title":"The Dipole Polarizability of Uracil in Aqueous Solution. A Sequential Monte Carlo/Quantum Mechanics Study","authors":"V. Ludwig, S. Canuto","doi":"10.1163/157404007782913138","DOIUrl":"https://doi.org/10.1163/157404007782913138","url":null,"abstract":"A combined and sequential Monte Carlo/quantum mechanics methodology is used to estimate the dipole polarizability of uracil in aqueous solution in normal thermodynamic conditions. Using the structures generated by the MC simulation, statistically uncorrelated configurations are sampled for subsequent quantum mechanical calculations using the central uracil molecule surrounded by the first solvation shell composed of 26 explicit water molecules. The dipole polarizability is obtained as an average value obtained from density-functional-theory calculations, using the B3P86 functional with varying basis sets. Statistically convergent result for the dipole polarizability of uracil in aqueous solution gives the average value of 100.1 ± 10.4 a03, indicating an increase of about 50% compared to the gas phase result.","PeriodicalId":101169,"journal":{"name":"Soft Computing Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82336595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1163/157404007782913363
K. Naka, F. Gu, Y. Aoki, S. Ohnishi
The elongation method designed for calculating the electronic structures of aperiodic polymers has been investigated in parallelization efficiency. The elongation finite-field method for determining (hypper)polarizabilities has been successfully applied to the three-dimensional urea crystal and its derivatives. It is shown that the elongation-FF method is suitable to large-scale calculations with parallelization and a powerful tool for nonlinear optical material designing.
{"title":"Parallelization Efficiency of the Elongation Method and its Application to NLO Design for Urea Crystal","authors":"K. Naka, F. Gu, Y. Aoki, S. Ohnishi","doi":"10.1163/157404007782913363","DOIUrl":"https://doi.org/10.1163/157404007782913363","url":null,"abstract":"The elongation method designed for calculating the electronic structures of aperiodic polymers has been investigated in parallelization efficiency. The elongation finite-field method for determining (hypper)polarizabilities has been successfully applied to the three-dimensional urea crystal and its derivatives. It is shown that the elongation-FF method is suitable to large-scale calculations with parallelization and a powerful tool for nonlinear optical material designing.","PeriodicalId":101169,"journal":{"name":"Soft Computing Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80991993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1163/157404007782913309
Pierre‐François Loos, A. Fornili, M. Sironi, X. Assfeld
We present a new quantum mechanics/molecular mechanics (QM/MM) scheme based on the Local-SCF method that avoids the extra-parametrization of the QM/MM frontier by taking into account the core electrons of the hybrid frontier atoms by means of self-consistent core orbitals (SCCO). This study follows and extends our previous investigation based on frozen core orbitals (FCO) [Chem. Phys. Lett. 427 236-240(2006)]. Test calculations on small organic compounds show that the most common atoms found in biochemical systems can be used as frontier atoms without adding any parameters, and that only relatively small geometric and energetic deviations compared to full-QM calculations are generated.
{"title":"Removing the extra frontier parameters in QM/MM methods: a tentative with the Local Self-Consistent Field method","authors":"Pierre‐François Loos, A. Fornili, M. Sironi, X. Assfeld","doi":"10.1163/157404007782913309","DOIUrl":"https://doi.org/10.1163/157404007782913309","url":null,"abstract":"We present a new quantum mechanics/molecular mechanics (QM/MM) scheme based on the Local-SCF method that avoids the extra-parametrization of the QM/MM frontier by taking into account the core electrons of the hybrid frontier atoms by means of self-consistent core orbitals (SCCO). This study follows and extends our previous investigation based on frozen core orbitals (FCO) [Chem. Phys. Lett. 427 236-240(2006)]. Test calculations on small organic compounds show that the most common atoms found in biochemical systems can be used as frontier atoms without adding any parameters, and that only relatively small geometric and energetic deviations compared to full-QM calculations are generated.","PeriodicalId":101169,"journal":{"name":"Soft Computing Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84123149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1163/157404007782913255
A. Hinchliffe, Mohamed Efhil, H. Soscún
We report Ab Initio energies, dipole moments and mean dipole polarizabilities for the ground and five lowest electronic excited singlet states of nitromethane, methylamine, nitromethylamine, nitrobenzene, aniline and p-nitroaniline, together with ground state data for methane and benzene. Ground state properties were calculated using the HF/6-311++G(2d,1p) model whilst excited states were modelled using CIS and CIS(D). Our ground state results are consistent with available experimental data and other advanced literature calculations. The XCH2Y calculations give group contributions of 13.6 atomic units (au) for NO2 and 7.7 au for NH2. The XC6H4Y 's suggest 14.4 and 10.8 au, but there is no evidence of a contribution from the push-pull mechanism. The excited state dipole moments and 's are consistent with the sparse experimental data, and we predict immensely enhanced values for these properties in many of the excited states.
{"title":"Ab Initio Studies of the Dipole Moments and Polarizabilities of p-nitroaniline and Related Molecules in their Ground and Excited States.","authors":"A. Hinchliffe, Mohamed Efhil, H. Soscún","doi":"10.1163/157404007782913255","DOIUrl":"https://doi.org/10.1163/157404007782913255","url":null,"abstract":"We report Ab Initio energies, dipole moments and mean dipole polarizabilities for the ground and five lowest electronic excited singlet states of nitromethane, methylamine, nitromethylamine, nitrobenzene, aniline and p-nitroaniline, together with ground state data for methane and benzene. Ground state properties were calculated using the HF/6-311++G(2d,1p) model whilst excited states were modelled using CIS and CIS(D). Our ground state results are consistent with available experimental data and other advanced literature calculations. The XCH2Y calculations give group contributions of 13.6 atomic units (au) for NO2 and 7.7 au for NH2. The XC6H4Y 's suggest 14.4 and 10.8 au, but there is no evidence of a contribution from the push-pull mechanism. The excited state dipole moments and 's are consistent with the sparse experimental data, and we predict immensely enhanced values for these properties in many of the excited states.","PeriodicalId":101169,"journal":{"name":"Soft Computing Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73276416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1163/157404007782913390
H. Sekino, N. Matsumura, Y. Sengoku
NMR chemical shifts are evaluated by the Fragment Molecular Orbital (FMO) method. Several practical approximations for the method are tested for water oligomer and poly-chloroprene. The FMO method reproduces the value by the ab-initio method without approximation and the experimental values. The adjacent approximation in fragment pair correction is found to be useful for qualitative prediction of NMR chemical shift in large bio-molecular systems, while monomer approximation fails in predicting the shielding constants of nuclei especially near the division for fragmentation. Preliminary application of the method with low level basis set to a bio-molecule indicates encouraging results for using the method as a theoretical tool in molecular biology.
{"title":"Evaluation of NMR Chemical Shift by Fragment Molecular Orbital Method","authors":"H. Sekino, N. Matsumura, Y. Sengoku","doi":"10.1163/157404007782913390","DOIUrl":"https://doi.org/10.1163/157404007782913390","url":null,"abstract":"NMR chemical shifts are evaluated by the Fragment Molecular Orbital (FMO) method. Several practical approximations for the method are tested for water oligomer and poly-chloroprene. The FMO method reproduces the value by the ab-initio method without approximation and the experimental values. The adjacent approximation in fragment pair correction is found to be useful for qualitative prediction of NMR chemical shift in large bio-molecular systems, while monomer approximation fails in predicting the shielding constants of nuclei especially near the division for fragmentation. Preliminary application of the method with low level basis set to a bio-molecule indicates encouraging results for using the method as a theoretical tool in molecular biology.","PeriodicalId":101169,"journal":{"name":"Soft Computing Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77120778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1163/157404007782913273
L. Balbás
The combination of Langevin molecular dynamics for simulated annealing with realistic quantum-mechanical interactions obtained from first principles supercell calculations within the pseudo potential plane-wave method are applied to examine the structural and electronic properties of the following systems i) pure and mixed GenTem (n, m = 0 - 2), Ge3, Te3 and Ge3Te3 semiconductor clusters, and ii) bimetallic PbNan (n ≤ 7) clusters. Results using the local density approximation (LDA) and the generalized gradient approximation (GGA) for the exchange correlation functional are compared with available experimental data. It is found that the GGA leads to larger bond lengths and smaller binding energies than the LDA, but both approximations lead to the same group symmetry for the ground state of these clusters. Two isomeric configurations for PbNa6, having C3v and Oh symmetries, respectively, are found. The dipole moments of semiconductor clusters are compared with those estimated from recent experiments at room temperature. The dipole moments from GGA calculations are, on average, in better agreement with experiments than those calculated with the LDA.
结合Langevin分子动力学模拟退火与伪势平方波方法中第一性原理超级单体计算获得的真实量子力学相互作用，研究了以下系统的结构和电子特性:i)纯和混合GenTem (n, m = 0 - 2)， Ge3, Te3和Ge3Te3半导体团簇，ii)双金属PbNan (n≤7)团簇。用局部密度近似(LDA)和广义梯度近似(GGA)计算交换相关泛函的结果与已有的实验数据进行了比较。结果表明，与LDA相比，GGA的键长更大，结合能更小，但两种近似的基态基对称性相同。发现了PbNa6的两种同分异构体构型，分别具有C3v和Oh对称。将半导体团簇的偶极矩与最近在室温下的实验结果进行了比较。平均而言，GGA计算得到的偶极矩比LDA计算得到的偶极矩更符合实验结果。
{"title":"First-Principles Langevin Molecular Dynamics Studies of Metallic and Semiconductor Clusters: GGA versus LDA Results","authors":"L. Balbás","doi":"10.1163/157404007782913273","DOIUrl":"https://doi.org/10.1163/157404007782913273","url":null,"abstract":"The combination of Langevin molecular dynamics for simulated annealing with realistic quantum-mechanical interactions obtained from first principles supercell calculations within the pseudo potential plane-wave method are applied to examine the structural and electronic properties of the following systems i) pure and mixed GenTem (n, m = 0 - 2), Ge3, Te3 and Ge3Te3 semiconductor clusters, and ii) bimetallic PbNan (n ≤ 7) clusters. Results using the local density approximation (LDA) and the generalized gradient approximation (GGA) for the exchange correlation functional are compared with available experimental data. It is found that the GGA leads to larger bond lengths and smaller binding energies than the LDA, but both approximations lead to the same group symmetry for the ground state of these clusters. Two isomeric configurations for PbNa6, having C3v and Oh symmetries, respectively, are found. The dipole moments of semiconductor clusters are compared with those estimated from recent experiments at room temperature. The dipole moments from GGA calculations are, on average, in better agreement with experiments than those calculated with the LDA.","PeriodicalId":101169,"journal":{"name":"Soft Computing Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78953415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1163/157404007782913408
J. Kobus
This article presents the numerical, finite difference, Hartree-Fock method as a source of reference values of total energies, multipole moments, static polarizabilities and hyperpolarizabilities (αzz, βzzz, γzzzz, Az,zz and Bzz,zz) for atoms and diatomic molecules. The finite field method is used to evaluate polarizabilities and hyperpolarizabilities as derivatives of the dipole and quadrupole moments with respect to the field. The finite difference calculations are compared with other numerical and finite basis set results. Since the finite difference Hartree-Fock method is capable of producing multipole moments with 10-12 significant figure accuracy the high quality of (hyper)polarizability values can be guaranteed.
{"title":"Hartree-Fock limit values of multipole moments, polarizabilities and hyperpolarizabilities for atoms and diatomic molecules","authors":"J. Kobus","doi":"10.1163/157404007782913408","DOIUrl":"https://doi.org/10.1163/157404007782913408","url":null,"abstract":"This article presents the numerical, finite difference, Hartree-Fock method as a source of reference values of total energies, multipole moments, static polarizabilities and hyperpolarizabilities (αzz, βzzz, γzzzz, Az,zz and Bzz,zz) for atoms and diatomic molecules. The finite field method is used to evaluate polarizabilities and hyperpolarizabilities as derivatives of the dipole and quadrupole moments with respect to the field. The finite difference calculations are compared with other numerical and finite basis set results. Since the finite difference Hartree-Fock method is capable of producing multipole moments with 10-12 significant figure accuracy the high quality of (hyper)polarizability values can be guaranteed.","PeriodicalId":101169,"journal":{"name":"Soft Computing Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87400267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1163/157404007782913444
M. Ghosh, K. Hazra, S. Bhattacharyya
The linear and non-linear optical response properties of 2-D quantum dots with two interacting carrier electrons having triplet coupling of spins are computed and compared with their singlet counterparts. The significant dependence of the response properties on the spin multiplicity in the high and low field regimes are sought to be rationalized.
{"title":"Response Properties of 2-Electron 2-D Quantum Dots: Triplet Versus Singlet.","authors":"M. Ghosh, K. Hazra, S. Bhattacharyya","doi":"10.1163/157404007782913444","DOIUrl":"https://doi.org/10.1163/157404007782913444","url":null,"abstract":"The linear and non-linear optical response properties of 2-D quantum dots with two interacting carrier electrons having triplet coupling of spins are computed and compared with their singlet counterparts. The significant dependence of the response properties on the spin multiplicity in the high and low field regimes are sought to be rationalized.","PeriodicalId":101169,"journal":{"name":"Soft Computing Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83931493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1163/157404007782913453
Hideaki Takahashi, M. Kitaura, R. Kishi, Suguru Ohta, Rika Okaji, S. Furukawa, M. Nakano
We compute the static polarizabilities of formaldehyde and ethylene in water solution by means of the QM/MM simulations and the polarizable continuum model for the purpose to examine the dependence of the polarizability on the method to include solvent effects. It is found that the polarizability of formaldehyde as well as ethylene is hardly changed by the solvent modeled by QM/MM approach. The results are reasonably consistent with suggestions given by other theoretical investigations which revealed that polarizabilities of a monomer in the linear hydrogen bonded chain is not increased by the hydrogen bondings. In contrast to the QM/MM method, it turns out that the polarizabilities are clearly enhanced for the solutes embedded in the dielectric continuums though both methods indicate that the σ electrons dominantly contribute to the polarizability.
{"title":"Theoretical Study on the Polarizabilities of Molecules in Solution by the Quantum Mechanical/Molecular Mechanical Approach: Comparison with the Polarizable Continuum Model","authors":"Hideaki Takahashi, M. Kitaura, R. Kishi, Suguru Ohta, Rika Okaji, S. Furukawa, M. Nakano","doi":"10.1163/157404007782913453","DOIUrl":"https://doi.org/10.1163/157404007782913453","url":null,"abstract":"We compute the static polarizabilities of formaldehyde and ethylene in water solution by means of the QM/MM simulations and the polarizable continuum model for the purpose to examine the dependence of the polarizability on the method to include solvent effects. It is found that the polarizability of formaldehyde as well as ethylene is hardly changed by the solvent modeled by QM/MM approach. The results are reasonably consistent with suggestions given by other theoretical investigations which revealed that polarizabilities of a monomer in the linear hydrogen bonded chain is not increased by the hydrogen bondings. In contrast to the QM/MM method, it turns out that the polarizabilities are clearly enhanced for the solutes embedded in the dielectric continuums though both methods indicate that the σ electrons dominantly contribute to the polarizability.","PeriodicalId":101169,"journal":{"name":"Soft Computing Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83207378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-03-06DOI: 10.1163/157404007779994214
M. M. Oliva, M. R. Delgado, J. Casado, M. Raposo, A. Fonseca, H. Hartmann, V. Hernández, J. Navarrete
A series of push-pull chromophores built around thiophene-based π-conjugating spacers and bearing various types of amino-donors and cyanovinyl-acceptors have been analyzed by means of UV-Vis-NIR spectroscopic measurements. Density functional theory (DFT) calculations have also been performed to help the assignment of the most relevant electronic features and to derive useful information about the molecular structure of these NLO-phores. The effects of the donor/acceptor substitution in the electronic and molecular properties of the π -conjugated spacer have been addressed. The effectiveness of the intramolecular charge transfer (ICT) has also been tested as a function of the nature of the end groups (i.e., electron-donating or electron-withdrawing capabilities).
{"title":"Quantum Chemical DFT and Spectroscopic UV-Vis-NIR Analysis of a Series of Push-Pull Oligothiophenes End-Capped by Amino/Cyanovinyl Groups","authors":"M. M. Oliva, M. R. Delgado, J. Casado, M. Raposo, A. Fonseca, H. Hartmann, V. Hernández, J. Navarrete","doi":"10.1163/157404007779994214","DOIUrl":"https://doi.org/10.1163/157404007779994214","url":null,"abstract":"A series of push-pull chromophores built around thiophene-based π-conjugating spacers and bearing various types of amino-donors and cyanovinyl-acceptors have been analyzed by means of UV-Vis-NIR spectroscopic measurements. Density functional theory (DFT) calculations have also been performed to help the assignment of the most relevant electronic features and to derive useful information about the molecular structure of these NLO-phores. The effects of the donor/acceptor substitution in the electronic and molecular properties of the π -conjugated spacer have been addressed. The effectiveness of the intramolecular charge transfer (ICT) has also been tested as a function of the nature of the end groups (i.e., electron-donating or electron-withdrawing capabilities).","PeriodicalId":101169,"journal":{"name":"Soft Computing Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85159944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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