NBO介绍要点课件

NaturalBondOrbital(NBO)EthaneC-Cbondin1,2,and3dimensions1.NBO概念、理论基本思想2.NBO程序介绍3.Gaussian&ADF中NBO功能的使用4.NBOVIEW程序介绍1.NBO概念、理论基本思想任何量子化学中，对指定电荷在空间内不同区域分布的划分方案关键是定义分子中的原子子空间。量子化学研究的一个重要的对象就是多原子分子体系中各原子的电子组态和静电荷分布，分子中的原子电荷分布对于从化学的角度去解释分子波函数，理解化学变化的内在本质有十分重要的作用。但是对于原子电荷和轨道的电荷密度布居进行定量的量子化学计算时，即使使用精确的基组函数,往往难以得到满意的结果。自然键轨道分析（NaturalBondOrbitalanalysis）是由AlanE.Reed,WeinstockandWeinhold在1984年提出的作为研究多原子分子体系中的杂化和共价效应的方法。与传统的Mülliken布居分析方法相比，自然键轨道分析方法受Löwdin的对称转换思想启发，采用正交的矩阵去避免结果的无实际意义的负轨道占据值。因而自然键轨道分析方法在描绘电子组态和原子上的静电荷方面的计算结果与实验结果更加吻合。NBO对HF、相关波函数及DFT方法均适用。自然键轨道是局域的少中心轨道（通常典型的为1或2，偶尔更多），在理想的紧凑形式下，描述电子对路易斯类似的分子成键模式（或在开壳情况下为单独的电子）。更确切的说，NBOs是一系列正交化的局域“最大占据”轨道，其包含的N/2部分（或在开壳情况下的N部分）给出总的N电子密度最精确可能的路易斯类似描述。

NBOs由NHOs{hA}组成，每个都形成一个优化的在指定中心的NAOs线性组合hA=Σk

akΘk(A)与NAOs类似，NHOs形成一个遍及整个基本空间的完全的正交化系列。核NBOs（在NBO输出中标记为“CR”)典型几乎为纯的NAO特征。单中心的“孤对”（非键）NBOs

nA（在NBO输出中标记为“LP”）各自由一个单独的规范NHO组成nA=hA双中心键NBOsΩAB(在NBO输出中标记为“BD”)为两个成键NHOs

hA,hB线性组合形成，对应于经典的Mulliken和Lennard-Jones键轨道形式，

ΩAB=aAhA+aBhB

其极化系数aA,aB满足aA2+aB2=1。依据这些系数值，一个成键NBO可能处于共价(aA=aB)和离子(aA>>aB)键限度之间。然而，在高极化形式(aA>>aB)的双中心ΩAB和单中心nA(aA=1,aB=0)之间没有明显的区别。为了与一般化学用法一致，只要在一个单中心上的电子密度达到95%或更多时(aA2≥0.95)，NBO程序确定一个高极化ΩAB为孤对nA。每一项NBO中，价层杂化hA,hB必须由相应的外部的反键NBOΩ*AB(在NBO输出中标记为“BD*”)正交地补充。

Ω*AB=aBhA−aAhB

价层反键Ω*AB为非路易斯类型，在基态的NLS描述中没有作用，特别项“antibond”反键源自相同产生成键NBOs的未充满价基杂化，因此Ω*AB's代表相应原子未用的价层容量，未被共价形式饱和。Ω*AB's被发现是典型的最重要的非路易斯"acceptor"轨道，对共振稳定性、分子间氢键和其他形式的超分子给体－受体结合起贡献。可得到的Ω*AB形状和能量知识是理解超出理想的路易斯结构描述的重要的"非共价"和"离域"现象的关键。价基非路易斯NBOs{Ω*AB}被一系列"Rydberg-type"单中心NBOs

rA（在程序输出中标价为"RY*"）所补充使NBO基础完善。与额外价NAOs来源类似，这些NBOs显然有可忽略的占据，因为考虑化学的目的能够被忽略。因此，显著占据的NBOs的有效延伸减至NAOs的NMB部分，与化学知识一致。

2.NBO程序介绍KeywordParms?KeywordDescriptionAOINFONWriteAObasisinformationtoLFN31ARCHIVEOWriteARCHIVE(FILE47)forstand-aloneGENNBOinputBNDIDXNNAO-WibergBondIndexandrelatedvalencyindicesFILEYSpecifyfilestemforPLOTfilesPLOTNWritefilesfororbitalplotting

3CBONDNSearchfor3-centerNBOs

ControlOptionsMainProgramOptions

KeywordParms?

KeywordDescription

Page

[BEND]O.Hybriddirectionalityand"bond-bending"analysisCMOO.BondingcharacterofcanonicalmolecularorbitalsDIPOLEO.Dipolemomentanalysis[E2PERT]O.2nd-orderperturbativeestimatesofNBOinteractionsNBBPO.Naturalbond-bondpolarizabilityindices[NBO]NNaturalbondorbitalcompositions[NBOSUM]N.NBOsummarytableNCSO.NaturalchemicalshieldinganalysisNJCO.NaturalJ-couplinganalysisNLMONNaturallocalizedmolecularorbitalcompositions[NPA]NNaturalpopulationanalysisNRTNNaturalresonancetheoryanalysisSTERICO.Naturalstericanalysis3CHBN3-c,4-ehyperbondsearchKeywordsinbracketsdenote[default]optionsthatareperformedevenifthe$NBOkeylistisempty.Notethatsomeoptionsautomaticallyturnonotherkeywordsthatareneededtoperformtheanalysis(e.g.,NLMOisautomaticallyturnedonforDIPOLE,NCS,orNJCanalysis).Usethevariouscontroloptionkeywords(suchasthePRINTorthresholdkeywords)tofurthercontroloutputfromeachmainprogramoption.

NBOTranslatesAccurateCalculationsIntoChemicalInsightsChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…NaturalPopulationAnalysisChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…SummaryofNaturalPopulationAnalysis: NaturalPopulation NaturalAtom# ChargeCoreValenceRydbergTotalC1 -0.440791.999004.438480.003316.44079N2 -0.897151.999535.893780.003847.89715H3 0.183700.000000.814530.001770.81630H4 0.217130.000000.781920.000960.78287H5 0.217130.000000.781920.000960.78287H6 0.359990.000000.638790.001220.64001H7 0.359990.000000.638790.0012 0.64001=======================================================================*Total* 0.000003.9985313.988200.0132818.00000****SampleOutput****thenaturalpopulationsaresummarizedasaneffectivevalenceelectronconfiguration("naturalelectronconfiguration")foreachatom:Atom#NaturalElectronConfigurationC1[core]2s(1.09)2p(3.35)N2[core]2s(1.43)2p(4.47)H31s(0.81)H41s(0.78)H51s(0.78)H61s(0.64)H71s(0.64)NATURALBONDORBITALS(Summary): PrincipalDelocalizationsNBO Occupancy Energy (geminal,vicinal,remote)=======================================================================Molecularunit1(CH3NO)1.BD(1)H1-N3 1.99309 -0.89250 32(v),20(v)2.BD(1)H2-N3 1.99322 -0.87920 3(v),19(v),32(v),21(v)3.BD(1)N3-C4 1.99828 -1.10527 29(g),28(g)4.BD(1)C4-O5 1.99925 -0.50592 31(g),16(v)5.BD(2)C4-O5 1.99802 -1.40674 19(g),28(v)6.BD(1)C4-H6 1.98929 -0.75792 29(v),23(v),15(v)7.CR(1)N3 1.99922 -15.31924 20(v),19(v),13(v),14(v)8.CR(1)C4 1.99939 -11.16963 27(v),29(v),28(v)9.CR(1)O5 1.99963 -20.09206 19(v),25(g),20(v)10.LP(1)N3 1.80683 -0.39458 31(v),22(v11.LP(1)O5 1.98262 -0.93620 19(v),20(v),33(v),30(v) 29(r)12.LP(2)O5 1.88568 -0.40982 30(v),33(v),20(v)****SampleOutput****NBOSummaryChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…1.H1-N3•NBOType

N-Hsigmabond

•HybridComposition

0.5390(s)H+0.8423(sp2.23)N•Occupancy

1.99309

e

NaturalBondOrbitalAnalysisChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…(Occupancy)Bondorbital/Coefficients/Hybrids1.(1.99309)BD(1)H1-N3 (29.05%)0.5390*H1s(100.00%) -1.0000-0.0010 (70.95%)0.8423*N3s(30.92%)p2.23(69.08%) 0.0002-0.5561-0.00200.68790.0155 -0.46600.0088-0.00010.00002.(1.99322)BD(1)H2-N3 (28.52%)0.5341*H2s(100.00%) -1.0000-0.0043 (71.48%)0.8454*N3s(30.20%)p2.31(69.80%) 0.0001-0.5495-0.00090.11580.0158 0.82730.00520.00000.0000****SampleOutput****(Occupancy)Bondorbital/Coefficients/Hybrids1.(1.99309)BD(1)H1-N3 (29.05%)0.5390*H1s(100.00%) -1.0000-0.0010 (70.95%)0.8423*N3s(30.92%)p2.23(69.08%) 0.0002-0.5561-0.00200.68790.0155 -0.46600.0088-0.00010.00002.(1.99322)BD(1)H2-N3 (28.52%)0.5341*H2s(100.00%) -1.0000-0.0043 (71.48%)0.8454*N3s(30.20%)p2.31(69.80%) 0.0001-0.5495-0.00090.11580.0158 0.82730.00520.00000.0000****SampleOutput****1.H1-N3•NBOType

N-Hsigmabond

•HybridComposition

0.5390(s)H+0.8423(sp2.23)N•Occupancy

1.99309e

NaturalBondOrbitalAnalysisChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…BondOrdersChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…1.241.001.79NaturalBondOrder:(total/covalent/ionic)Atom123456

1.Ht0.00200.00000.99590.00000.0000

0.0000c0.00000.57870.00000.0000

0.0000i0.00000.41720.00000.0000

0.00002.Ht0.00000.00500.99280.00000.0000

0.0000c0.00000.56640.00000.0000

0.0000i0.00000.42650.00000.0000

0.00003.Nt0.99590.99280.76911.24220.00000.0000c0.57870.56640.75190.00000.0000i0.41720.42650.49030.00000.00004.Ct0.00000.00001.24220.00001.79040.9674c0.00000.00000.75191.09670.7956i0.00000.00000.49030.69370.17195.Ot0.00000.0000

0.00001.79042.20760.0000c0.00000.0000

0.00001.09670.0000i0.00000.0000

0.00000.69370.00006.Ht0.00000.0000

0.00000.96740.00000.0275c0.00000.0000

0.00000.79560.0000i0.00000.0000

0.00000.17190.0000****SampleOutput****H1-N3:0.58Covalent+0.42Ionic=1.00TotalN3-C4:0.75Covalent+0.49Ionic=1.24TotalC4-O5:1.10Covalent+0.69Ionic=1.79TotalWibergbondindexWibergbondindexmatrixintheNAObasis:Atom1234567

1.C0.00000.94030.94030.94280.99820.00220.00222.H0.94030.00000.00110.00050.00550.00050.00723.H0.94030.00110.00000.00050.00550.00720.00054.H0.94280.00050.00050.00000.02580.00010.00015.N0.99820.00550.00550.02580.00000.85640.85646.H0.00220.00050.00720.00010.85640.00000.00037.H0.00220.00720.00050.00010.85640.00030.0000****SampleOutput****PerturbationTheoryEnergyAnalysisChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…SECONDORDERPERTURBATIONTHEORYANALYSISOFFOCKMATRIXINNBOBASISThresholdforprinting:0.50kcal/mol E(2)E(j)-E(i)F(i,j)DonorNBO(i) AcceptorNBO(j) kcal/mola.u.a.u.==========================================================================withinunit11.BD(1)H1-N3 20.RY*(2)C4 2.541.890.0621.BD(1)H1-N3 32.BD*(2)C4-O5 4.411.740.0782.BD(1)H2-N3 19.RY*(1)C4 2.101.760.0542.BD(1)H2-N3 21.RY*(3)C4 0.592.320.0332.BD(1)H2-N3 32.BD*(2)C4-O5 1.281.720.0422.BD(1)H2-N3 33.BD*(1)C4-H6 2.451.530.0553.BD(1)N3-C4 28.BD*(1)H1-N3 0.641.760.0303.BD(1)N3-C4 29.BD*(1)H2-N3 0.711.760.0324.BD(1)C4-O5 16.RY*(2)N3 0.891.900.0374.BD(1)C4-O5 31.BD*(1)C4-O5 0.950.670.0245.BD(2)C4-O5 19.RY*(1)C4 1.832.290.0585.BD(2)C4-O5 28.BD*(1)H1-N3 1.592.060.0516.BD(1)C4-H6 15.RY*(1)N3 0.652.810.0386.BD(1)C4-H6 23.RY*(1)O5 1.612.790.0606.BD(1)C4-H6 29.BD*(1)H2-N3 5.241.420.077****SampleOutput****(C4-H6)*(H2-N3)stabilization5.24kcal/mol(2ndorderestimate)NaturalChemicalShielding(NCS)Analysis

ChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…NaturalNMRChemicalShieldingTensorAnalysisNCSTensoranalysisisusing 8624wordsThresholdforprinting:0.10ppmSummaryofisotropicNMRchemicalshieldingTotalLewis(L)andnon-Lewis(NL)contributions:(ppm)NBO C(1)N(2)H(3)H(4)H(5)H(6)H(7)

1.C1-N2L-6.546.390.560.500.502.412.41NL0.17-0.350.030.080.08-0.09-0.092.C1-H3L-4.210.5026.521.851.850.100.10NL-0.61-0.390.07-0.05-0.05-0.01-0.013.C1-H4L-2.642.112.1025.732.040.130.21NL-0.21-1.42-0.010.050.04-0.04-0.084.C1-H5L-2.642.112.102.0425.730.210.13NL-0.21-1.42-0.010.040.05-0.08-0.045.N2-H6L0.097.190.340.290.2422.873.36NL-0.010.17-0.02-0.12-0.010.03-0.04****SampleOutput****The(C1-N2)bondde-shieldsthecarbonby6.54ppmandshieldsthenitrogenby6.39ppm.NaturalResonanceTheory(NRT)Improvements

ChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…

ResonanceRS Weight(%) Added(Removed)1*(2) 69.362* 24.39 N3-C4,(C4-O5),(N3),O53 2.37 (N3-C4),C4-O5,N3,(O5)4(2) 1.99 C4-O5,(C4-H6),(O5),H65(2) 0.76 N3-C4,(C4-H6),(N3),H66 0.36 (H2-N3),N3-C4,(C4-H6),H27 0.16 (H1-N3),N3-C4,(C4-O5),O58 0.15 (H2-N3),N3-C4,(C4-O5),O59 0.14 (H1-N3),N3-C4,(C4-O5),H110 0.14 (H2-N3),N3-C4,N3-C4,(C4-O5), (C4-H6),H2,(N3),O511-15 0.17100.00*Total* [*=referencestructure]****SampleOutput****Togetthe2ndresonancestructurefromthe1st:

AddabondbetweenN3andC4

RemoveabondbetweenC4andO5

RemovealonepaironN3andaddalonepairtoO5NewFeaturesinNBO5.0CanonicalMolecularOrbital(CMO)Analysis

NaturalChemicalShielding(NCS)Analysis

NaturalJ-Coupling(NJC)Analysis

3-center,4-eHyperbond(3CHB)Search

LargerSystems(999atoms，9999basisfunctionatmost,200atoms,2000basisfunctionindefault)NaturalResonanceTheory(NRT)Improvements

NaturalLocalizedMolecularOrbital(NLMO)Improvements

STERICImprovement

NewCheckpointingOptions

NewMatrixOutputOptions

TransitionMetalHybridDirectionality

BasisLinearDependencyDetection/Protection

NewPC-WindowsGENNBOStand-AloneVersion

/~nbo5/

3.NBO-AffiliatedElectronicStructureSystems

andProtectedInterfacesSystem(*)Vendor/DistributorJaguar

(1)Schrodinger,Inc.Q-Chem

(1)Q-Chem,Inc.PQS

(1)ParallelQuantumSystemsNWChem

(1)PacificNorthwestNationalLaboratoriesADF(1)ScientificComputing&ModellingN.V.PCGAMESS(2)AlexA.Granovsky,MoscowStateUniversityGAMESS(U.S.)(3)AmesLaboratories,IowaStateUniversityGaussian98/03

(4)Gaussian,Inc.(1)NBO5.0is/willbeincluded.(2)NBO5.0included,butrequiresNBOpasswordfromTCI/NBOSoftware(3)Protectedinterface;requireslinkingtoNBO5.0fromTCI/NBOSoftware.(4)NBO3.1included,butcanbeupgradedwithNBO5.0fromTCI/NBOSoftware.Adfnbo,gennbo:NBOanalysisGENNBO-supportedoptionsincludeallkeywordsexceptthoseexplicitlyrequiringinteractivecommunicationwiththehostelectronicstructuresystem(viz.,$DELdeletions,NEDA,NCS,NJC).GENNBO"communicates"withtheoriginalADFcalculationthroughanarchivefile(JOB.47file,preservingallnecessarydetailsofthefinaldensity)thatisinitiallygeneratedbyADFandsubsequentlybecomestheinputfileforGENNBO.NBOinADFFULLFOCKAOMAT2FILESAVETAPE15EndInputEor$ADFBIN/adfnbo<<eor

调用nbo模块eorecho""echo""echo"ContentsofFILE47="echo""echo""catFILE47$ADFBIN/gennbo<FILE47产生。47文件作为进一步nbo分析的输入文件echo""echo""echo"Contentsofnbotmp.37="echo""echo""catnbotmp.37echo""echo""echo"Contentsofnbotmp.39="echo""echo""catnbotmp.39echo""ech