E. Sadurní, F. Leyvraz, T. Stegmann, T. Seligman, D. Klein
The accidental degeneracy appearing in cycloacenes as triplets and quadruplets is explained with the concept of segmentation, introduced here with the aim of describing the effective disconnection of $pi$ orbitals on these organic compounds. For periodic systems with time reversal symmetry, the emergent nodal domains are shown to divide the atomic chains into simpler carbon structures analog to benzene rings, diallyl chains, anthracene (triacene) chains and tetramethyl-naphtalene skeletal forms. The common electronic levels of these segments are identified as members of degenerate multiplets of the global system. The peculiar degeneracy of Mobius cycloacene is also explained by segmentation. In the last part, it is shown that the multiplicity of energies for cycloacene can be foreseen by studying the continuous limit of the tight-binding model; the degeneracy conditions are put in terms of Chebyshev polynomials. The results obtained in this work have important consequences on the physics of electronic transport in organic wires, together with their artificial realizations.
{"title":"Hidden duality and accidental degeneracy in cycloacene and Möbius cycloacene","authors":"E. Sadurní, F. Leyvraz, T. Stegmann, T. Seligman, D. Klein","doi":"10.1063/5.0031586","DOIUrl":"https://doi.org/10.1063/5.0031586","url":null,"abstract":"The accidental degeneracy appearing in cycloacenes as triplets and quadruplets is explained with the concept of segmentation, introduced here with the aim of describing the effective disconnection of $pi$ orbitals on these organic compounds. For periodic systems with time reversal symmetry, the emergent nodal domains are shown to divide the atomic chains into simpler carbon structures analog to benzene rings, diallyl chains, anthracene (triacene) chains and tetramethyl-naphtalene skeletal forms. The common electronic levels of these segments are identified as members of degenerate multiplets of the global system. The peculiar degeneracy of Mobius cycloacene is also explained by segmentation. In the last part, it is shown that the multiplicity of energies for cycloacene can be foreseen by studying the continuous limit of the tight-binding model; the degeneracy conditions are put in terms of Chebyshev polynomials. The results obtained in this work have important consequences on the physics of electronic transport in organic wires, together with their artificial realizations.","PeriodicalId":8439,"journal":{"name":"arXiv: Chemical Physics","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82236482","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 : 2020-08-03DOI: 10.21468/SCIPOSTCHEM.1.1.001
Klaas Gunst, D. Neck, P. Limacher, S. Baerdemacker
We employ tensor network methods for the study of the seniority quantum number - defined as the number of unpaired electrons in a many-body wave function - in molecular systems. Seniority-zero methods recently emerged as promising candidates to treat strong static correlations in molecular systems, but are prone to deficiencies related to dynamical correlation and dispersion. We systematically resolve these deficiencies by increasing the allowed seniority number using tensor network methods. In particular, we investigate the number of unpaired electrons needed to correctly describe the binding of the neon and nitrogen dimer and the $D_{6h}$ symmetry of benzene.
{"title":"The seniority quantum number in Tensor Network States","authors":"Klaas Gunst, D. Neck, P. Limacher, S. Baerdemacker","doi":"10.21468/SCIPOSTCHEM.1.1.001","DOIUrl":"https://doi.org/10.21468/SCIPOSTCHEM.1.1.001","url":null,"abstract":"We employ tensor network methods for the study of the seniority quantum number - defined as the number of unpaired electrons in a many-body wave function - in molecular systems. Seniority-zero methods recently emerged as promising candidates to treat strong static correlations in molecular systems, but are prone to deficiencies related to dynamical correlation and dispersion. We systematically resolve these deficiencies by increasing the allowed seniority number using tensor network methods. In particular, we investigate the number of unpaired electrons needed to correctly describe the binding of the neon and nitrogen dimer and the $D_{6h}$ symmetry of benzene.","PeriodicalId":8439,"journal":{"name":"arXiv: Chemical Physics","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73129144","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}
A method which casts the chemical source term computation into an artificial neural network (ANN)-inspired form is presented. This approach is well-suited for use on emerging supercomputing platforms that rely on graphical processing units (GPUs). The resulting equations allow for a GPU-friendly matrix-multiplication based source term estimation where the leading dimension (batch size) can be interpreted as the number of chemically reacting cells in the domain; as such, the approach can be readily adapted in high-fidelity solvers for which an MPI rank offloads the source term computation task for a given number of cells to the GPU. Though the exact ANN-inspired recasting shown here is optimal for GPU environments as-is, this interpretation allows the user to replace portions of the exact routine with trained, so-called approximate ANNs, where the goal of these approximate ANNs is to increase computational efficiency over the exact routine counterparts. Note that the main objective of this paper is not to use machine learning for developing models, but rather to represent chemical kinetics using the ANN framework. The end result is that little-to-no training is needed, and the GPU-friendly structure of the ANN formulation during the source term computation is preserved. The method is demonstrated using chemical mechanisms of varying complexity on both 0-D auto-ignition and 1-D channel detonation problems, and the details of performance on GPUs are explored.
{"title":"A Neural Network Inspired Formulation of Chemical Kinetics","authors":"S. Barwey, V. Raman","doi":"10.3390/en14092710","DOIUrl":"https://doi.org/10.3390/en14092710","url":null,"abstract":"A method which casts the chemical source term computation into an artificial neural network (ANN)-inspired form is presented. This approach is well-suited for use on emerging supercomputing platforms that rely on graphical processing units (GPUs). The resulting equations allow for a GPU-friendly matrix-multiplication based source term estimation where the leading dimension (batch size) can be interpreted as the number of chemically reacting cells in the domain; as such, the approach can be readily adapted in high-fidelity solvers for which an MPI rank offloads the source term computation task for a given number of cells to the GPU. Though the exact ANN-inspired recasting shown here is optimal for GPU environments as-is, this interpretation allows the user to replace portions of the exact routine with trained, so-called approximate ANNs, where the goal of these approximate ANNs is to increase computational efficiency over the exact routine counterparts. Note that the main objective of this paper is not to use machine learning for developing models, but rather to represent chemical kinetics using the ANN framework. The end result is that little-to-no training is needed, and the GPU-friendly structure of the ANN formulation during the source term computation is preserved. The method is demonstrated using chemical mechanisms of varying complexity on both 0-D auto-ignition and 1-D channel detonation problems, and the details of performance on GPUs are explored.","PeriodicalId":8439,"journal":{"name":"arXiv: Chemical Physics","volume":"139 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89218345","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 : 2020-07-22DOI: 10.1103/physrevresearch.2.043082
Vidushi Sharma, M. Fernández-Serra
In density functional-theoretic studies of photoionized water-based systems, the role of charge localization in proton-transfer dynamics is not well understood. This is due to the inherent complexity in extracting the contributions of coupled electron-nuclear non-adiabatic dynamics in the presence of exchange and correlation functional errors. In this work, we address this problem by simulating a model system of ionized linear H-bonded water clusters using real-time Time Dependent Density Functional Theory (rt-TDDFT)-based Ehrenfest dynamics. Our aim is to understand how self-interaction error in semilocal exchange and correlation functionals affects the probability of proton transfer. In particular, we show that for H-bonded (H$_2$O)$_n^+$ chains (with $n>3$), the proton-transfer probability attains a maximum, becoming comparable to that predicted by hybrid functionals. This is because the formation of hemibonded-type geometries is largely suppressed in extended H-bonded structures. We also show how the degree of localization of the initial photo-hole is connected to the probability of a proton-transfer reaction, as well as to the separation between electronic and nuclear charge. These results are compared to those obtained with adiabatic dynamics where the initial wavefunction is allowed to relax to the ground state of the ion cluster, explaining why different functionals and dynamical approaches lead to quantitatively different results.
{"title":"Proton-transfer dynamics in ionized water chains using real-time time-dependent density functional theory","authors":"Vidushi Sharma, M. Fernández-Serra","doi":"10.1103/physrevresearch.2.043082","DOIUrl":"https://doi.org/10.1103/physrevresearch.2.043082","url":null,"abstract":"In density functional-theoretic studies of photoionized water-based systems, the role of charge localization in proton-transfer dynamics is not well understood. This is due to the inherent complexity in extracting the contributions of coupled electron-nuclear non-adiabatic dynamics in the presence of exchange and correlation functional errors. In this work, we address this problem by simulating a model system of ionized linear H-bonded water clusters using real-time Time Dependent Density Functional Theory (rt-TDDFT)-based Ehrenfest dynamics. Our aim is to understand how self-interaction error in semilocal exchange and correlation functionals affects the probability of proton transfer. In particular, we show that for H-bonded (H$_2$O)$_n^+$ chains (with $n>3$), the proton-transfer probability attains a maximum, becoming comparable to that predicted by hybrid functionals. This is because the formation of hemibonded-type geometries is largely suppressed in extended H-bonded structures. We also show how the degree of localization of the initial photo-hole is connected to the probability of a proton-transfer reaction, as well as to the separation between electronic and nuclear charge. These results are compared to those obtained with adiabatic dynamics where the initial wavefunction is allowed to relax to the ground state of the ion cluster, explaining why different functionals and dynamical approaches lead to quantitatively different results.","PeriodicalId":8439,"journal":{"name":"arXiv: Chemical Physics","volume":"114 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77589289","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 : 2020-07-21DOI: 10.1021/acs.jpcc.0c05196.s001
S. Kulik, S. Pullanchery, S. Roke
The structures of interfaces of nano- and microscale objects in aqueous solution are important for a wide variety of physical, chemical and biological processes. Vibrational sum frequency scattering has emerged as a useful and unique probe of the interfacial structure of nano- and microscale objects in water. However, the full surface vibrational stretch mode spectrum has not been measured yet, even though it would be extremely informative to do so. The reason for this is that probing the vibrational modes of interfacial water requires a full understanding of how the linear absorptive properties of the bulk aqueous medium influence the sum frequency scattering process. Here, we have simulated vibrational sum frequency scattering spectra of the interface of nanoscale objects dispersed in water. We analyzed the effect of the infrared pulse absorption on the outcome of surface vibrational sum frequency scattering measurements. We find that both infrared absorption as well as the type of optical detection can drastically modify the measured vibrational interfacial spectrum. The observed changes comprise spectral distortion, frequency shifting of the main vibrational stretch mode and the introducing of a new high frequency peak. This last feature is enhanced by non-resonant interactions.
{"title":"Vibrational sum frequency scattering in absorptive media: A theoretical case study of nano-objects water","authors":"S. Kulik, S. Pullanchery, S. Roke","doi":"10.1021/acs.jpcc.0c05196.s001","DOIUrl":"https://doi.org/10.1021/acs.jpcc.0c05196.s001","url":null,"abstract":"The structures of interfaces of nano- and microscale objects in aqueous solution are important for a wide variety of physical, chemical and biological processes. Vibrational sum frequency scattering has emerged as a useful and unique probe of the interfacial structure of nano- and microscale objects in water. However, the full surface vibrational stretch mode spectrum has not been measured yet, even though it would be extremely informative to do so. The reason for this is that probing the vibrational modes of interfacial water requires a full understanding of how the linear absorptive properties of the bulk aqueous medium influence the sum frequency scattering process. Here, we have simulated vibrational sum frequency scattering spectra of the interface of nanoscale objects dispersed in water. We analyzed the effect of the infrared pulse absorption on the outcome of surface vibrational sum frequency scattering measurements. We find that both infrared absorption as well as the type of optical detection can drastically modify the measured vibrational interfacial spectrum. The observed changes comprise spectral distortion, frequency shifting of the main vibrational stretch mode and the introducing of a new high frequency peak. This last feature is enhanced by non-resonant interactions.","PeriodicalId":8439,"journal":{"name":"arXiv: Chemical Physics","volume":"68 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80343279","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 : 2020-07-13DOI: 10.26434/chemrxiv.12647033.v1
Sambit Das, S. Chakraborty, R. Ramakrishnan
First-principles calculation of the standard formation enthalpy, $Delta H_f^0$~(298K), in such large scale as required by chemical space explorations, is amenable only with density functional approximations (DFAs) and some composite wave function theories (cWFTs). Alas, the accuracies of popular range-separated hybrid, `rung-4' DFAs, and cWFTs that offer the best accuracy-vs.-cost trade-off have as yet been established only for datasets predominantly comprising small molecules, hence, their transferability to larger datasets remains vague. In this study, we present an extended benchmark dataset of over two-thousand values of $Delta H_f^0$ for structurally and electronically diverse molecules. We apply quartile-ranking based on boundary-corrected kernel density estimation to filter outliers and arrive at Probabilistically Pruned Enthalpies of 1908 compounds (PPE1908). For this dataset, we rank the prediction accuracies of G4(MP2), ccCA and 23 popular DFAs using conventional and probabilistic error metrics. We discuss systematic prediction errors and highlight the role an empirical higher-level correction (HLC) plays in the G4(MP2) model. Furthermore, we comment on uncertainties associated with the reference empirical data for atoms and systematic errors introduced by these that grow with the molecular size. We believe these findings to aid in identifying meaningful application domains for quantum thermochemical methods.
{"title":"Critical Benchmarking of the G4(MP2) Model, the Correlation Consistent Composite Approach and Popular Density Functional Approximations on a Probabilistically Pruned Benchmark Dataset of Formation Enthalpies","authors":"Sambit Das, S. Chakraborty, R. Ramakrishnan","doi":"10.26434/chemrxiv.12647033.v1","DOIUrl":"https://doi.org/10.26434/chemrxiv.12647033.v1","url":null,"abstract":"First-principles calculation of the standard formation enthalpy, $Delta H_f^0$~(298K), in such large scale as required by chemical space explorations, is amenable only with density functional approximations (DFAs) and some composite wave function theories (cWFTs). Alas, the accuracies of popular range-separated hybrid, `rung-4' DFAs, and cWFTs that offer the best accuracy-vs.-cost trade-off have as yet been established only for datasets predominantly comprising small molecules, hence, their transferability to larger datasets remains vague. In this study, we present an extended benchmark dataset of over two-thousand values of $Delta H_f^0$ for structurally and electronically diverse molecules. We apply quartile-ranking based on boundary-corrected kernel density estimation to filter outliers and arrive at Probabilistically Pruned Enthalpies of 1908 compounds (PPE1908). For this dataset, we rank the prediction accuracies of G4(MP2), ccCA and 23 popular DFAs using conventional and probabilistic error metrics. We discuss systematic prediction errors and highlight the role an empirical higher-level correction (HLC) plays in the G4(MP2) model. Furthermore, we comment on uncertainties associated with the reference empirical data for atoms and systematic errors introduced by these that grow with the molecular size. We believe these findings to aid in identifying meaningful application domains for quantum thermochemical methods.","PeriodicalId":8439,"journal":{"name":"arXiv: Chemical Physics","volume":"176 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82623445","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 : 2020-06-29DOI: 10.1103/physreva.102.062806
M. Lesiuk, M. Musiał, R. Moszynski
We report state-of-the-art ab initio calculations of the potential energy curve for the $a^3Sigma_u^+$ state of the lithium dimer conducted to achieve spectroscopic accuracy ($<$1cm$^{-1}$) without any prior adjustment to fit the corresponding experimental data. The nonrelativistic clamped-nuclei component of the interaction energy is calculated with a composite method involving six-electron coupled cluster and full configuration interaction theories combined with basis sets of Slater-type orbitals ranging in quality from double- to sextuple-zeta. To go beyond the nonrelativistic Born-Oppenheimer picture we include both the leading-order relativistic and adiabatic corrections, and find both of these effects to be non-negligible within the present accuracy standards. The potential energy curve developed by us allowed to calculate molecular parameters ($D_e$, $D_0$, $omega_e$ etc.) for this system, as well as the corresponding vibrational energy levels, with an error of only a few tenths of a wavenumber ($0.2-0.4,$cm$^{-1}$). We also report an ab initio value for the scattering length of two $^2S$ lithium atoms which determines the stability of the related Bose-Einstein condensate.
为了达到光谱精度($<$ 1cm $^{-1}$),无需事先调整以拟合相应的实验数据,我们报告了对锂二聚体$a^3Sigma_u^+$状态的势能曲线进行的最先进的从头计算。用一种复合方法计算了相互作用能的非相对论夹核分量,该方法涉及六电子耦合簇和全构型相互作用理论,并结合从双zeta到六zeta的slater型轨道基集。为了超越非相对论的玻恩-奥本海默图,我们包括了一级相对论和绝热修正,并发现这两种影响在目前的精度标准内都是不可忽略的。我们开发的势能曲线允许计算该系统的分子参数($D_e$, $D_0$, $omega_e$等),以及相应的振动能级,误差仅为波数的十分之一($0.2-0.4,$ cm $^{-1}$)。我们还报道了两个$^2S$锂原子的散射长度的从头计算值,这决定了相关玻色-爱因斯坦凝聚体的稳定性。
{"title":"Potential-energy curve for the \u0000a3Σu+\u0000 state of a lithium dimer with Slater-type orbitals","authors":"M. Lesiuk, M. Musiał, R. Moszynski","doi":"10.1103/physreva.102.062806","DOIUrl":"https://doi.org/10.1103/physreva.102.062806","url":null,"abstract":"We report state-of-the-art ab initio calculations of the potential energy curve for the $a^3Sigma_u^+$ state of the lithium dimer conducted to achieve spectroscopic accuracy ($<$1cm$^{-1}$) without any prior adjustment to fit the corresponding experimental data. The nonrelativistic clamped-nuclei component of the interaction energy is calculated with a composite method involving six-electron coupled cluster and full configuration interaction theories combined with basis sets of Slater-type orbitals ranging in quality from double- to sextuple-zeta. To go beyond the nonrelativistic Born-Oppenheimer picture we include both the leading-order relativistic and adiabatic corrections, and find both of these effects to be non-negligible within the present accuracy standards. The potential energy curve developed by us allowed to calculate molecular parameters ($D_e$, $D_0$, $omega_e$ etc.) for this system, as well as the corresponding vibrational energy levels, with an error of only a few tenths of a wavenumber ($0.2-0.4,$cm$^{-1}$). We also report an ab initio value for the scattering length of two $^2S$ lithium atoms which determines the stability of the related Bose-Einstein condensate.","PeriodicalId":8439,"journal":{"name":"arXiv: Chemical Physics","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84525067","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}