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Zhang K, Ren S, Caricato M. Multistate QM/QM Extrapolation of UV/Vis Absorption Spectra with Point Charge Embedding. J Chem Theory Comput 2020; 16:4361-4372. [DOI: 10.1021/acs.jctc.0c00339] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kaihua Zhang
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Sijin Ren
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Marco Caricato
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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Deng S, Zhiyong H, Mengjiao Z, Shuangqi F, Jingyuan Z, Yunzhen H, Hailuan X, Jinding C. Isolation and phylogenetic analysis of a new Porcine parvovirus strain GD2013 in China. J Virol Methods 2019; 275:113748. [PMID: 31605714 DOI: 10.1016/j.jviromet.2019.113748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/04/2019] [Accepted: 10/03/2019] [Indexed: 10/25/2022]
Abstract
Porcine parvovirus (PPV), a causative agent of an infectious reproductive disorder causing stillbirth, mummification, embryonic death and infertility (SMEDI) syndrome in swine, is a threat to both domestic pigs and wild boars regardless of age and gender. Recent studies found that the observed average substitution rate in the PPV genome was close to those of the RNA viruses and new strains showing serological neutralization activities different from that of the vaccine strain NADL-2 have been reported. These observations have increased the need for the development of new commercial vaccine strains. In this study, a new PPV strain, GD2013, was isolated from Guangdong, China, and its entire genome sequenced. A phylogenetic tree based on the complete coding region of the genomes of 32 PPV strains was constructed using the Bayesian Markov Chain Monte Carlo (MCMC) method. The results showed that strain GD2013 fell into the same phylogenetic cluster as the classical vaccine strains NADL-2 and POVCAP, suggesting a close relationship to the vaccine strains. Multiple sequence alignments and amino acid mutation analyses of the PPV VP2 gene revealed a new amino acid polymorphism site at Thr45 on VP2 that could be used to identify low virulence strains as vaccine candidates. Selective pressure analysis of the NS1 and VP2 genes by calculating the mean rates of non-synonymous substitutions (dN) over synonymous substitutions (dS) implied that both of these genes were under negative selection. Therefore, by using phylogenetic and amino acid mutation analyses, a likely candidate strain suitable for evaluation as an attenuated vaccine strain was identified.
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Affiliation(s)
- Shaofeng Deng
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou, 510640, China
| | - Han Zhiyong
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou, 510640, China
| | - Zhu Mengjiao
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou, 510640, China
| | - Fan Shuangqi
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou, 510640, China
| | - Zhang Jingyuan
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou, 510640, China
| | - Huang Yunzhen
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou, 510640, China
| | - Xu Hailuan
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou, 510640, China
| | - Chen Jinding
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou, 510640, China.
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Baudin P, Kristensen K. Correlated natural transition orbital framework for low-scaling excitation energy calculations (CorNFLEx). J Chem Phys 2017; 146:214114. [PMID: 28595400 PMCID: PMC5462619 DOI: 10.1063/1.4984820] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/18/2017] [Indexed: 11/15/2022] Open
Abstract
We present a new framework for calculating coupled cluster (CC) excitation energies at a reduced computational cost. It relies on correlated natural transition orbitals (NTOs), denoted CIS(D')-NTOs, which are obtained by diagonalizing generalized hole and particle density matrices determined from configuration interaction singles (CIS) information and additional terms that represent correlation effects. A transition-specific reduced orbital space is determined based on the eigenvalues of the CIS(D')-NTOs, and a standard CC excitation energy calculation is then performed in that reduced orbital space. The new method is denoted CorNFLEx (Correlated Natural transition orbital Framework for Low-scaling Excitation energy calculations). We calculate second-order approximate CC singles and doubles (CC2) excitation energies for a test set of organic molecules and demonstrate that CorNFLEx yields excitation energies of CC2 quality at a significantly reduced computational cost, even for relatively small systems and delocalized electronic transitions. In order to illustrate the potential of the method for large molecules, we also apply CorNFLEx to calculate CC2 excitation energies for a series of solvated formamide clusters (up to 4836 basis functions).
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Affiliation(s)
- Pablo Baudin
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Kasper Kristensen
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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Baudin P, Kjærgaard T, Kristensen K. CC2 oscillator strengths within the local framework for calculating excitation energies (LoFEx). J Chem Phys 2017; 146:144107. [PMID: 28411600 DOI: 10.1063/1.4979713] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In a recent work [P. Baudin and K. Kristensen, J. Chem. Phys. 144, 224106 (2016)], we introduced a local framework for calculating excitation energies (LoFEx), based on second-order approximated coupled cluster (CC2) linear-response theory. LoFEx is a black-box method in which a reduced excitation orbital space (XOS) is optimized to provide coupled cluster (CC) excitation energies at a reduced computational cost. In this article, we present an extension of the LoFEx algorithm to the calculation of CC2 oscillator strengths. Two different strategies are suggested, in which the size of the XOS is determined based on the excitation energy or the oscillator strength of the targeted transitions. The two strategies are applied to a set of medium-sized organic molecules in order to assess both the accuracy and the computational cost of the methods. The results show that CC2 excitation energies and oscillator strengths can be calculated at a reduced computational cost, provided that the targeted transitions are local compared to the size of the molecule. To illustrate the potential of LoFEx for large molecules, both strategies have been successfully applied to the lowest transition of the bivalirudin molecule (4255 basis functions) and compared with time-dependent density functional theory.
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Affiliation(s)
- Pablo Baudin
- qLEAP Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Thomas Kjærgaard
- qLEAP Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Kasper Kristensen
- qLEAP Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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Biancardi A, Barnes J, Caricato M. Point charge embedding for ONIOM excited states calculations. J Chem Phys 2017; 145:224109. [PMID: 27984901 DOI: 10.1063/1.4972000] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hybrid quantum mechanical methods can assist in the interpretation and prediction of the electronic spectra of large molecular structures. In this work, we study the performance of the ONIOM (Our own N-layered Integrated molecular Orbital molecular Mechanics) hybrid method for the calculation of transition energies and oscillator strengths by embedding the core region in a field of fixed point charges. These charges introduce polarization effects from the substituent groups to the core region. We test various charge definitions, with particular attention to the issue of overpolarization near the boundary between layers. To minimize this issue, we fit the charges on the electrostatic potential of the entire structure in the presence of the link atoms used to cap dangling bonds. We propose two constrained fitting strategies: one that produces an average set of charges common to both model system calculations, EE(L1), and one that produces two separate sets of embedding charges, EE(L2). The results from our tests show that indeed electronic embedding with constrained-fitted charges tends to improve the performance of ONIOM compared to non-embedded calculations. However, the EE(L2) charges work best for transition energies, and the EE(L1) charges work best for oscillator strengths. This may be an indication that fixed point charges do not have enough flexibility to adapt to each system, and other effects (e.g., polarization of the embedding field) may be necessary.
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Affiliation(s)
- Alessandro Biancardi
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | - Jeremy Barnes
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | - Marco Caricato
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
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Ren S, Caricato M. Multi-state extrapolation of UV/Vis absorption spectra with QM/QM hybrid methods. J Chem Phys 2016; 144:184102. [PMID: 27179466 DOI: 10.1063/1.4948471] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this work, we present a simple approach to simulate absorption spectra from hybrid QM/QM calculations. The goal is to obtain reliable spectra for compounds that are too large to be treated efficiently at a high level of theory. The present approach is based on the extrapolation of the entire absorption spectrum obtained by individual subcalculations. Our program locates the main spectral features in each subcalculation, e.g., band peaks and shoulders, and fits them to Gaussian functions. Each Gaussian is then extrapolated with a formula similar to that of ONIOM (Our own N-layered Integrated molecular Orbital molecular Mechanics). However, information about individual excitations is not necessary so that difficult state-matching across subcalculations is avoided. This multi-state extrapolation thus requires relatively low implementation effort while affording maximum flexibility in the choice of methods to be combined in the hybrid approach. The test calculations show the efficacy and robustness of this methodology in reproducing the spectrum computed for the entire molecule at a high level of theory.
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Affiliation(s)
- Sijin Ren
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr., Lawrence, Kansas 66045, USA
| | - Marco Caricato
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr., Lawrence, Kansas 66045, USA
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7
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 734] [Impact Index Per Article: 81.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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Chung LW, Hirao H, Li X, Morokuma K. The ONIOM method: its foundation and applications to metalloenzymes and photobiology. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.85] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Caricato M, Vreven T, Trucks GW, Frisch MJ. Oscillator Strengths in ONIOM Excited State Calculations. J Chem Theory Comput 2010; 7:180-7. [DOI: 10.1021/ct1006289] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Caricato
- Gaussian, Inc., 340 Quinnipiac St., Bldg. 40, Wallingford, Connecticut 06492, United States, and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Thom Vreven
- Gaussian, Inc., 340 Quinnipiac St., Bldg. 40, Wallingford, Connecticut 06492, United States, and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Gary W. Trucks
- Gaussian, Inc., 340 Quinnipiac St., Bldg. 40, Wallingford, Connecticut 06492, United States, and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Michael J. Frisch
- Gaussian, Inc., 340 Quinnipiac St., Bldg. 40, Wallingford, Connecticut 06492, United States, and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
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