The photophysics of 3-dimethylamino-2-methyl-propenal (DMAMP) after excitation to the S2 (ππ^*) electronic state was studied using the resonance Raman spectroscopy and complete active space self-consistent fiel...The photophysics of 3-dimethylamino-2-methyl-propenal (DMAMP) after excitation to the S2 (ππ^*) electronic state was studied using the resonance Raman spectroscopy and complete active space self-consistent field method calculations. The transition barriers of the ground state tautomerization reactions between DMAMP and its three isomers were determined at B3LYP/6-311++G(d,p) level of theory. The vibrational spectra were assigned. The A- band resonance Raman spectra were obtained in acetonitrile with excitation wavelengths in resonance with the first intense absorption band to probe the structural dynamics of DMAMP. The B3LYP-TD computation was carried out to determine the relative A-band resonance Raman intensities of the fundamental modes, and the result indicated that the vibronic-coupling existed in Franck-Condon region. Complete active space self-consistent field (CASSCF) calculations were carried out to determine the excitation energies of the lower-lying singlet and triplet excited states, the conical intersection points and the intersystem crossing points. The A-band short-time structural dynamics and the corresponding decay dynamics of DMAMP were obtained by analysis of the resonance Raman intensity pattern and CASSCF computations. It was found that a sudden de-conjugation between C1=O6 and C2=C3 occurred at the Franck-Condon region of the S2(ππ^*) state, while the enhancement of the conjugation interaction between C3 and N(CH3)2, and between C1 and C2 evolutions shortly after the wavepacket leaves away the Pranck-Condon region via the excited state charge redistribution. The de-conjugation interaction between C1=O6 and C2=C3 made the rotation of C3=N(CH3)2 group around the C2-C3 bond much easier, while the enhanced conjugation between C1 and C2, and between C3 and N(CH3)2 made the rotation around the C1-C2 bond and C3-N5 more difficult. It was revealed that the initial structural dynamics of DMAMP was predominantly towards the CI-I(S2/S0) point, while the opportunities towards either CI-2(S2/S0) or CI-3(S2/S0) point were negligible. Two decay channels of DMAMP from S2,FC(ππ^*) to So or Tl,min via various CIs and ISCs were proposed.展开更多
Agonist binding of A2A adenosine receptor (A2AAR) shows protective effects against inflammatory and immune. Efforts are exerted in understanding the general mechanism and developing A2AAR selectively binding agonist...Agonist binding of A2A adenosine receptor (A2AAR) shows protective effects against inflammatory and immune. Efforts are exerted in understanding the general mechanism and developing A2AAR selectively binding agonists. Using molecular dynamics (MD) simula- tions, we have studied the interactions between A2AAR and its agonist (adenosine), and analyzed the induced dynamic behaviors of the receptor. Key residues interacting with adenosine are identified: A63^2.61,I66^2.64,V84^3.32,L85^3.33,T88^3.36,F168^5.29,M177^5.38,L249^6.51,H250^6.52 and N253^6.55 interacting with adenosine with affinities larger than 0.5 kcal/mol. Moreover, no interaction between adenosine and L167^5.28 is observed, which supports our previous findings that L1675^5.28 is an antagonist specific binding reside. The dynamic be- haviors of agonist bound A2AAR are found to be different from apo-A2AAR in three typical functional switches: (i) tight "ionic lock" forms in adenosine-A2AAR, but it is in equilibrium between formation and breakage in apo-A2AAR; (ii) the "rotamer toggle switch", T88^3.36/F242^6.44/W246^6.48, adopted different rotameric conformations in adenosin-A2AAR and apo-A2AAR; (iii) adenosine-A2AAR has a flexible intracellular loop 2 (IC2) and s-helical IC3, while apo-A2AAR preferred s-helical IC2 and flexible IC3. Our results indicate that agonist binding induced different conformational rearrangements of these characteristic functional switches in adenosine-A2AAR and apo-A2AAR.展开更多
The complex model of Thermus thermophilus xylose isomerase (TtXI) with D-xylose was constructed, and molecular dynamics (MD) simulations were carried out at 300 and 360 K for 10 ns by NAMD2.5. The radius of gyrati...The complex model of Thermus thermophilus xylose isomerase (TtXI) with D-xylose was constructed, and molecular dynamics (MD) simulations were carried out at 300 and 360 K for 10 ns by NAMD2.5. The radius of gyration (Rg), subunit interactions, and residue flexibility were analyzed. The results show that residues 60-69, 142-148, 169-172, and 332-340 have high flexibility at 300 and 360 K. Residues with higher flexibility at 360 K than that at 300 K can mainly be divided into two groups: one locates in the helix-loophelix region consisting of residues 55-80 in catalytic domain; the other at subunit interfaces. The Rg of catalytic domain at 360 K shows 0.16 A higher than that at 300 K, but Rg of small C-terminal domain has no obvious difference. The results indicate that enhanced Rg of catalytic domain may lead to the intense motion of the active site of TtXI and promote the D-xylose isomization reaction. Eight hydrogen bonds and five ion pairs are reduced at subunit interfaces at 360 K compared with 300 K, that may be the main reason for the decrease in rigidity and increase in activity at high temperature of TtXI. This result also help to explain the cold-adaption phenomenon of TtXI E372G mutant reported previously. Our results reveal the relationship between temperature and structure flexibility of TtXI, and play an important role in understanding the thermostability of thermophile protein with multiple subunits.展开更多
Results of researches on study of the kinetics and isomerization mechanism of the alkyladamantanes in the presence of the heterogeneous catalysts of the acid type are considered as detection and experimental proof of ...Results of researches on study of the kinetics and isomerization mechanism of the alkyladamantanes in the presence of the heterogeneous catalysts of the acid type are considered as detection and experimental proof of a new intramolecular rearrangement of the carbcations bridged alicyclic hydrocarbons--2,4-moving of the methyl groups (β-methyl shift). The proof of realization of such rearrangement is direct and primary formation 1,4-dimethyladamantane from 1,2-dimethyladamatane, passing a formation stage of the thermodynamic much stable 1,3-dimethyladamantane; direct formation 1,3,6-trimethyladamantane from 1,3,4-trimethyladamantane, excepting a formation stage 1,3.5-trimethyladamantane, and also other isomers which formation is impossible to explain by means of known 1,2-methyl shift (a-methyl shift).展开更多
We perform accurate quantum dynamcs calculations on the isomerization of vinylidene-acetylene.Large-scale parallel computations are accomplished by an efficient theoretical scheme developed by our group,in which the b...We perform accurate quantum dynamcs calculations on the isomerization of vinylidene-acetylene.Large-scale parallel computations are accomplished by an efficient theoretical scheme developed by our group,in which the basis functions are customized for the double-H transfer process.The A_(1)' and B_(2)'' vinylidene and delocalization states are obtained.The peaks recently observed in the cryo-SEVI spectra are analyzed,and very good agreement for the energy levels is achieved between theory and experiment.The discrepancies of energy levels between our calculations and recent experimental cryo-SEVI spectra are of similar magnitudes to the experimental error bars,or≤30 cm^(-1) excluding those involving the excitation of the CCH_(2) scissor mode.A kind of special state,called the isomerization state,is revealed and reported,which is characterized by large probability densities in both vinylidene and acetylene regions.In addition,several states dominated by vinylidene character are reported for the first time.The present work would contribute to the understanding of the double-H transfer.展开更多
The aim of this study was to assess the runoff amount from a catchment characterized by diverse land uses by using the Soil Conservation Service Curve Number(SCS-CN) method based on Curve Number(CN) defined for domina...The aim of this study was to assess the runoff amount from a catchment characterized by diverse land uses by using the Soil Conservation Service Curve Number(SCS-CN) method based on Curve Number(CN) defined for dominant homogeneous elementary sub-regions.The calculations employed the SCS-CN method,involving the division of the catchment in two homogeneous parts and determining the runoff amount.The obtained results were compared with the results provided by three other CN determination methods,i.e.the Hawkins function,the kinetics equation,and a complementary error function peak.The catchment is located in a mountain dominated by forest land cover.Empirical CN-Precipitation(CN_(emp)-P) data pairs were analyzed using the mentioned methods,and the highest quality score was achieved from model 1.The results suggest that dividing a catchment into two homogeneous areas and determining their separate CN parameters,used later on to calculate the runoff by means of the presented approach,could be an alternative to the standard methods.The described method is relatively easy,and as it does not require an adoption of numerous parameters,and it can be employed for designing hydraulic facilities.展开更多
A pharmacokinetic comparison of gossypol isomers in cattle was made by investigating their transfer from ingested food to plasma and their degradation by rumen microbes. The gossypol isomers in whole cottonseed, plasm...A pharmacokinetic comparison of gossypol isomers in cattle was made by investigating their transfer from ingested food to plasma and their degradation by rumen microbes. The gossypol isomers in whole cottonseed, plasma, and rumen fluid were determined by high-performance liquid chromatography(HPLC). The intakes of(+)-and(-)-gossypol by cows on three farms were about 5.6–8.5 and 3.8–5.9 g/(d·herd), respectively. The plasma gossypol concentrations increased as ingestion increased and ranged from 0.31 to 0.48 μg/ml for the(+) form and from 0.39 to 0.59 μg/ml for the(-) form. The(+) form was slightly predominant(58.8%–59.8%) in the gossypol ingested by the cows, whereas the(-) form predominated(54.6%–55.9%) in the plasma. An in vitro study showed that at 6 h, 67.4% and 85.7% of the(-)-gossypol were degraded in 500 and 1000 μg/g treatment groups, respectively, and these increased to 83.6% and 92.5%, respectively, at 12 h. The regularity of the degradation of(+)-gossypol was similar to that of(-)-gossypol. These results showed that(-)-gossypol may be more persistent than(+)-gossypol in plasma, and that the degradation of the gossypol isomers in the rumen is rapid and not enantioselective in cattle.展开更多
In opinion dynamics,the convergence of the heterogeneous Hegselmann-Krause(HK) dynamics has always been an open problem for years which looks forward to any essential progress.In this short note,we prove a partial con...In opinion dynamics,the convergence of the heterogeneous Hegselmann-Krause(HK) dynamics has always been an open problem for years which looks forward to any essential progress.In this short note,we prove a partial convergence conclusion of the general heterogeneous HK dynamics.That is,there must be some agents who will reach static states in finite time,while the other opinions have to evolve between them with a minimum distance if all the opinions does not reach consensus.And this result leads to the convergence of several special cases of heterogeneous HK dynamics,including when the minimum confidence bound is large enough,the initial opinion difference is small enough,and so on.展开更多
This paper presents two aggregation strategies in convex intersection region for the distributed mobile sensor network(MSN) with heterogeneous dynamics. First, the authors analyze individual local perception model and...This paper presents two aggregation strategies in convex intersection region for the distributed mobile sensor network(MSN) with heterogeneous dynamics. First, the authors analyze individual local perception model and dynamics model, set the intersection of all the local perceptions as the region of interest(ROI). The MSN consists of sensors with first-order dynamics and second-order dynamics. Then, the authors design a control strategy to ensure that individuals aggregate at a point in the ROI relying on their local perceptions and the locations of neighbors within their communication scope. The authors describe this situation of aggregation as rendezvous. In addition, the authors introduce artificial potential field to make sensors deploy dispersedly in a bounded range near the ROI,which the authors call dispersed deployment. Finally, the authors prove the stability of the proposed strategies and validate the theoretical results by simulations. This research is applied for the cooperative deployment and data collection of mobile platforms with different dynamics under the condition of inaccurate perception.展开更多
Using molecular dynamics with embedded-atom-type interatomicpotentials, we simulated the melting behavior of a spherical Ag3055 cluster coated with Ni. The semi-coherent Ag/Ni interface formed at low temperatures acts...Using molecular dynamics with embedded-atom-type interatomicpotentials, we simulated the melting behavior of a spherical Ag3055 cluster coated with Ni. The semi-coherent Ag/Ni interface formed at low temperatures acts as an effective barrier against the surface melting and leads to a substantial superheating of the Ag cluster. The melting point was found to be about 100 K above the equilibrium melting point of the bulk Ag crystal (1230 K±15 K) and about 290 K above that (1040 K) of the free Ag3055 cluster. A superheating of 70 K was observed in the high-temperature differential scanning calorimetry measurement for Ag particles with a mean size of 30 nm embedded in Ni matrix prepared by means of melt-spinning. Melting is initiated locally at the defective interfacial area and then propagates inwards, suggesting a heterogeneously nucleated melting event at the Ag/Ni interface.展开更多
基金ACKNOWLEDGMENTS This work was supported by the National Natural Science Foundation of China (No.21033002 and No.21202032) and the National Basic Research Program of China (No.2013CB834604).
文摘The photophysics of 3-dimethylamino-2-methyl-propenal (DMAMP) after excitation to the S2 (ππ^*) electronic state was studied using the resonance Raman spectroscopy and complete active space self-consistent field method calculations. The transition barriers of the ground state tautomerization reactions between DMAMP and its three isomers were determined at B3LYP/6-311++G(d,p) level of theory. The vibrational spectra were assigned. The A- band resonance Raman spectra were obtained in acetonitrile with excitation wavelengths in resonance with the first intense absorption band to probe the structural dynamics of DMAMP. The B3LYP-TD computation was carried out to determine the relative A-band resonance Raman intensities of the fundamental modes, and the result indicated that the vibronic-coupling existed in Franck-Condon region. Complete active space self-consistent field (CASSCF) calculations were carried out to determine the excitation energies of the lower-lying singlet and triplet excited states, the conical intersection points and the intersystem crossing points. The A-band short-time structural dynamics and the corresponding decay dynamics of DMAMP were obtained by analysis of the resonance Raman intensity pattern and CASSCF computations. It was found that a sudden de-conjugation between C1=O6 and C2=C3 occurred at the Franck-Condon region of the S2(ππ^*) state, while the enhancement of the conjugation interaction between C3 and N(CH3)2, and between C1 and C2 evolutions shortly after the wavepacket leaves away the Pranck-Condon region via the excited state charge redistribution. The de-conjugation interaction between C1=O6 and C2=C3 made the rotation of C3=N(CH3)2 group around the C2-C3 bond much easier, while the enhanced conjugation between C1 and C2, and between C3 and N(CH3)2 made the rotation around the C1-C2 bond and C3-N5 more difficult. It was revealed that the initial structural dynamics of DMAMP was predominantly towards the CI-I(S2/S0) point, while the opportunities towards either CI-2(S2/S0) or CI-3(S2/S0) point were negligible. Two decay channels of DMAMP from S2,FC(ππ^*) to So or Tl,min via various CIs and ISCs were proposed.
文摘Agonist binding of A2A adenosine receptor (A2AAR) shows protective effects against inflammatory and immune. Efforts are exerted in understanding the general mechanism and developing A2AAR selectively binding agonists. Using molecular dynamics (MD) simula- tions, we have studied the interactions between A2AAR and its agonist (adenosine), and analyzed the induced dynamic behaviors of the receptor. Key residues interacting with adenosine are identified: A63^2.61,I66^2.64,V84^3.32,L85^3.33,T88^3.36,F168^5.29,M177^5.38,L249^6.51,H250^6.52 and N253^6.55 interacting with adenosine with affinities larger than 0.5 kcal/mol. Moreover, no interaction between adenosine and L167^5.28 is observed, which supports our previous findings that L1675^5.28 is an antagonist specific binding reside. The dynamic be- haviors of agonist bound A2AAR are found to be different from apo-A2AAR in three typical functional switches: (i) tight "ionic lock" forms in adenosine-A2AAR, but it is in equilibrium between formation and breakage in apo-A2AAR; (ii) the "rotamer toggle switch", T88^3.36/F242^6.44/W246^6.48, adopted different rotameric conformations in adenosin-A2AAR and apo-A2AAR; (iii) adenosine-A2AAR has a flexible intracellular loop 2 (IC2) and s-helical IC3, while apo-A2AAR preferred s-helical IC2 and flexible IC3. Our results indicate that agonist binding induced different conformational rearrangements of these characteristic functional switches in adenosine-A2AAR and apo-A2AAR.
基金This work was supported by the National Natural Science Foundation of China (No.20336010) and the State Key Basic Research and Development Plan of China (No.2003CB716000).
文摘The complex model of Thermus thermophilus xylose isomerase (TtXI) with D-xylose was constructed, and molecular dynamics (MD) simulations were carried out at 300 and 360 K for 10 ns by NAMD2.5. The radius of gyration (Rg), subunit interactions, and residue flexibility were analyzed. The results show that residues 60-69, 142-148, 169-172, and 332-340 have high flexibility at 300 and 360 K. Residues with higher flexibility at 360 K than that at 300 K can mainly be divided into two groups: one locates in the helix-loophelix region consisting of residues 55-80 in catalytic domain; the other at subunit interfaces. The Rg of catalytic domain at 360 K shows 0.16 A higher than that at 300 K, but Rg of small C-terminal domain has no obvious difference. The results indicate that enhanced Rg of catalytic domain may lead to the intense motion of the active site of TtXI and promote the D-xylose isomization reaction. Eight hydrogen bonds and five ion pairs are reduced at subunit interfaces at 360 K compared with 300 K, that may be the main reason for the decrease in rigidity and increase in activity at high temperature of TtXI. This result also help to explain the cold-adaption phenomenon of TtXI E372G mutant reported previously. Our results reveal the relationship between temperature and structure flexibility of TtXI, and play an important role in understanding the thermostability of thermophile protein with multiple subunits.
文摘Results of researches on study of the kinetics and isomerization mechanism of the alkyladamantanes in the presence of the heterogeneous catalysts of the acid type are considered as detection and experimental proof of a new intramolecular rearrangement of the carbcations bridged alicyclic hydrocarbons--2,4-moving of the methyl groups (β-methyl shift). The proof of realization of such rearrangement is direct and primary formation 1,4-dimethyladamantane from 1,2-dimethyladamatane, passing a formation stage of the thermodynamic much stable 1,3-dimethyladamantane; direct formation 1,3,6-trimethyladamantane from 1,3,4-trimethyladamantane, excepting a formation stage 1,3.5-trimethyladamantane, and also other isomers which formation is impossible to explain by means of known 1,2-methyl shift (a-methyl shift).
基金supported by the National Natural Science Foundation of China(No.21973098 and No.22133003)the Youth Innovation Promotion Association CAS(No.2018045)the Beijing National Laboratory for Molecular Sciences。
文摘We perform accurate quantum dynamcs calculations on the isomerization of vinylidene-acetylene.Large-scale parallel computations are accomplished by an efficient theoretical scheme developed by our group,in which the basis functions are customized for the double-H transfer process.The A_(1)' and B_(2)'' vinylidene and delocalization states are obtained.The peaks recently observed in the cryo-SEVI spectra are analyzed,and very good agreement for the energy levels is achieved between theory and experiment.The discrepancies of energy levels between our calculations and recent experimental cryo-SEVI spectra are of similar magnitudes to the experimental error bars,or≤30 cm^(-1) excluding those involving the excitation of the CCH_(2) scissor mode.A kind of special state,called the isomerization state,is revealed and reported,which is characterized by large probability densities in both vinylidene and acetylene regions.In addition,several states dominated by vinylidene character are reported for the first time.The present work would contribute to the understanding of the double-H transfer.
基金Dean of the Faculty of Environmental Engineering and Land Surveying, University of Agriculture in Krakow, for financial support
文摘The aim of this study was to assess the runoff amount from a catchment characterized by diverse land uses by using the Soil Conservation Service Curve Number(SCS-CN) method based on Curve Number(CN) defined for dominant homogeneous elementary sub-regions.The calculations employed the SCS-CN method,involving the division of the catchment in two homogeneous parts and determining the runoff amount.The obtained results were compared with the results provided by three other CN determination methods,i.e.the Hawkins function,the kinetics equation,and a complementary error function peak.The catchment is located in a mountain dominated by forest land cover.Empirical CN-Precipitation(CN_(emp)-P) data pairs were analyzed using the mentioned methods,and the highest quality score was achieved from model 1.The results suggest that dividing a catchment into two homogeneous areas and determining their separate CN parameters,used later on to calculate the runoff by means of the presented approach,could be an alternative to the standard methods.The described method is relatively easy,and as it does not require an adoption of numerous parameters,and it can be employed for designing hydraulic facilities.
基金Project supported by the National Natural Science Foundation of China(No.31472123)
文摘A pharmacokinetic comparison of gossypol isomers in cattle was made by investigating their transfer from ingested food to plasma and their degradation by rumen microbes. The gossypol isomers in whole cottonseed, plasma, and rumen fluid were determined by high-performance liquid chromatography(HPLC). The intakes of(+)-and(-)-gossypol by cows on three farms were about 5.6–8.5 and 3.8–5.9 g/(d·herd), respectively. The plasma gossypol concentrations increased as ingestion increased and ranged from 0.31 to 0.48 μg/ml for the(+) form and from 0.39 to 0.59 μg/ml for the(-) form. The(+) form was slightly predominant(58.8%–59.8%) in the gossypol ingested by the cows, whereas the(-) form predominated(54.6%–55.9%) in the plasma. An in vitro study showed that at 6 h, 67.4% and 85.7% of the(-)-gossypol were degraded in 500 and 1000 μg/g treatment groups, respectively, and these increased to 83.6% and 92.5%, respectively, at 12 h. The regularity of the degradation of(+)-gossypol was similar to that of(-)-gossypol. These results showed that(-)-gossypol may be more persistent than(+)-gossypol in plasma, and that the degradation of the gossypol isomers in the rumen is rapid and not enantioselective in cattle.
基金supported by the National Natural Science Foundation of China(Grant No.11371049)Fundamental Research Funds for the Central Universities(Grant No.2016JBM070)
文摘In opinion dynamics,the convergence of the heterogeneous Hegselmann-Krause(HK) dynamics has always been an open problem for years which looks forward to any essential progress.In this short note,we prove a partial convergence conclusion of the general heterogeneous HK dynamics.That is,there must be some agents who will reach static states in finite time,while the other opinions have to evolve between them with a minimum distance if all the opinions does not reach consensus.And this result leads to the convergence of several special cases of heterogeneous HK dynamics,including when the minimum confidence bound is large enough,the initial opinion difference is small enough,and so on.
基金supported by the National Natural Science Foundation of China under Grant No.61203078the Foundation for Innovative Research Groups of the National Natural Science Foundation of China under Grant No.61321002+3 种基金the Projects of Major International(Regional)Joint Research Program NSFC under Grant No.61120106010the Beijing Education Committee Cooperation Building Foundation Projectthe Program for Changjiang Scholars and Innovative Research Team in University under Grant No.IRT1208the Chang Jiang Scholars Program,and the Beijing Outstanding Ph.D.Program Mentor under Grant No.20131000704
文摘This paper presents two aggregation strategies in convex intersection region for the distributed mobile sensor network(MSN) with heterogeneous dynamics. First, the authors analyze individual local perception model and dynamics model, set the intersection of all the local perceptions as the region of interest(ROI). The MSN consists of sensors with first-order dynamics and second-order dynamics. Then, the authors design a control strategy to ensure that individuals aggregate at a point in the ROI relying on their local perceptions and the locations of neighbors within their communication scope. The authors describe this situation of aggregation as rendezvous. In addition, the authors introduce artificial potential field to make sensors deploy dispersedly in a bounded range near the ROI,which the authors call dispersed deployment. Finally, the authors prove the stability of the proposed strategies and validate the theoretical results by simulations. This research is applied for the cooperative deployment and data collection of mobile platforms with different dynamics under the condition of inaccurate perception.
基金This work was supported by the Ministry of Science and Technology of China (Grant No. 1999064505)the National Natural Science Foundation of China (Grant Nos. 59801011, 59931030 and 59841004) the Max-Planck-Society of Germany.
文摘Using molecular dynamics with embedded-atom-type interatomicpotentials, we simulated the melting behavior of a spherical Ag3055 cluster coated with Ni. The semi-coherent Ag/Ni interface formed at low temperatures acts as an effective barrier against the surface melting and leads to a substantial superheating of the Ag cluster. The melting point was found to be about 100 K above the equilibrium melting point of the bulk Ag crystal (1230 K±15 K) and about 290 K above that (1040 K) of the free Ag3055 cluster. A superheating of 70 K was observed in the high-temperature differential scanning calorimetry measurement for Ag particles with a mean size of 30 nm embedded in Ni matrix prepared by means of melt-spinning. Melting is initiated locally at the defective interfacial area and then propagates inwards, suggesting a heterogeneously nucleated melting event at the Ag/Ni interface.